I wonder if the problem is from starting with too coarse a grit. Tools, including particles of abrasive grit, can cause sub-surface deformation in metals and I wonder if it applies to wood as well.
I ran into that when I operated a small metallography lab in a nuclear facility. I embedded aluminum sample plates in epoxy. The thin plates were bonded by heat and pressure and my job was to grind the samples flat, polish and etch them, then examine with a microscope. I found if I first quickly flattened a potted sample with a very coarse grit disk then didn't remove enough material with successively finer grits, invisible damage from the coarse grits would remain in the aluminum just below the surface, only to be revealed in the later polishing stages. If I spent a little more time with the intermediate grits, this didn't happen.
I'm wondering if particles of very coarse grit might deform the subsurface of softer woods (sort of like a line of tearout) and be visible later, maybe when finish is applied. I've never seen this in wood but I rarely start with grits coarser than 320. Maybe prepare some test surfaces of side and end grain, start sanding the entire sample as usual, then sand one section as you do normally and spend a little more time with intermediate grits on another section. See if there is a difference when the finish is applied. I do this with quadrants of a squarish platter to demonstrate the effect of following the NRS with hand scraping.
Even if not using coarse grits, could the sandpaper used be a problem? I've tried lots of different types and some seemed to be less consistent. I finally found a type I'm happy with.
Also, what you described about seeing a scratch with your eyes but not in a photo: assuming the lighting is equivalent, could that be since the eyes see in stereo and the camera lens is mono? Maybe try looking at a scratch with one eye closed and see if there's a visible difference. Or twist your head 90-deg and see if the scratch looks the same.
These are wild ideas - it's hard to diagnose a visual thing through words! If possible, find a local mentor whose surfaces you like, get them to look at one of your surfaces where you see rogue scratches, and ask what they think. If possible, let them watch you work. With luck, maybe there will be an AhHa moment or at least get some ideas.
I knew a turner who was having all kinds of problems getting nice surfaces. When I watched him turn it was immediately obvious - in his case the problem was simply tools that were not sharp enough! His problem had nothing to do with the scratch problem you mentioned, but still, a second person might spot something.
JKJ
Some very interesting thoughts.
I have been wondering if this is solely a softer wood problem, or if I've seen it occur on harder woods. I'll have to experiment more. My current experience, the reason I started the thread, is the woods are on the softer side. The holly is probably one of the softest woods I have turned in the last year. I have some maple that is also softer, and a few others I'll be turning soon here that are...softish. I recently turned a number of eggs for easter, and, some were softish/medium, others were rather hard woods. One I actually don't have an identity for (I'll post a photo and see if someone can id), and, I don't actually recall having scratch issues with it. Its kind of a semi-figured, rather chatoyant piece of wood from a cutoff, that I bought just because they were selling the chunk for like two bucks, and I thought I saw hints of some rippled figure in it (which I did!) and wanted to do something with it. It was quite hard, turning it wasn't easy...BUT, I don't recall having any real issues sanding it to a real nice smooth surface.
On the first holly bowl, I accidentally just barely toughed my gouge to the outside at one point...the bowl wasn't spinning, but I'd just sharpened the gouge, and it left a mark. I sanded the mark out, but, there ARE subsurface fibers that appear to be damaged. I sanded it for a while, and the defect didn't entirely go away. Its diminished enough that it looks like a characteristic of the grain now, although I can see it, and I can tell its some damage to fibers that go deep enough, that I would have to over-thin the walls to fully and entirely remove it. So on woods as soft as Holly, I do think that subsurface damage (other than tearout) can occur. Now, the touch from the gouge was accidental. I am wondering now, though, if that's what's happening with the scratch marks...
For sandpaper. Early on, I kind of went scatterbrained, and I bought and tried every kind of sandpaper I could. I tried all the ones WW sell, several kinds of discs that Woodcraft sells, Abranet, various kinds of abrasive pads (the 3M types, which are mostly abrasive bonded to metal fibers), and then various kinds of sheet sandpapers. In the long run, I converged on just two types: Norton and Klingspor. I don't have a ready source of Klingspor locally, so I have to order it, while Woodcraft carries Norton. I have found the Norton seems to be far more effective than the other types I've used, except maybe Abranet (although, Abranet, the mesh stuff, sometimes has its own challenges). Norton seems to leave fewer scratches...I think that was the main reason I converged mostly on it, almost every other abrasive I used left WORSE scratches, especially the WW discs. It may just be a technique thing, but, norton with lighter pressure just seems to sand much more effectively, and has a lesser problem than I've experienced in the past. Klingspor seems to be about the same, however, I don't know that I've explored all the Klingspor options (since I have to order, and I haven't really had a chance to look at all the Klingspor options in person; I've heard some people mention fabric backed Klingspor, but I've only used paper backed.)
I do use Abranet some times. Its the mesh stuff, and I have boxes of the stuff, ranging from their coarsest to I think 1500 or 2000 grit. I like and don't like it.

This stuff has a "grain" or a "direction" itself...in one direction its ridgid and cannot really be folded, in the other it rolls up or folds very easily. There are advantages to that, and it can be problematic. I used to use some of the lowish grits when I really had bad tearout to deal with, as the dust would go right through the paper and it seemed faster at correcting the issue. However, I have put a lot of effort lately into turning without tearout. As I mentioned in other communications to you, I do sometimes still get tearout, although these days, its a tiny fraction of the problem it used to be (I'm a total perfectionist, if you haven't figured that out yet!

) So, I don't have to sand much to correct tearout, and for the most part, I try to correct it by other means...sheer scraping and scraping mostly. I think I am mostly successful too, and if I have to sand tearout out, it really doesn't take much effort or time these days. I had a little bit with the two holly bowls I've been working on, but I started sanding at 220, and it was gone in less than a minute. The thing that remains, then, is the scratch marks...
Regarding tools, thanks mostly to you, I believe my tools are quite sharp. They are sharper today, than I think they ever have been. I am not honing or stropping, only because I don't really have an effective means of doing that. I have a stroping pad, that I use for honing my plane irons, and I tried to use that on one of my gouges, and I promptly gouged a strip right out of the leather. :'( If I had a belt on a powered wheel, like the Tormek, I'd hone for sure, but ATM its the only thing I am not doing. I am sharpening on the 600 grit wheel now, and my edges are really nice. They might not be perfectly shaped, working on that. but they seem truly sharp now. Cutting the wood with a gouge is so easy, especially the M42 steel with my Carter & Son gouges. Now, one of the main tools I've been using is an HSS/M2 steel gouge I ground to a 40/40 shape, using Stu Batty's method of grinding (on a platform with 40 degree lines top mark the limits.)
I don't know if there is something wrong with this particular gouge, or if this is just the nature of HSS/M2 steel, but this gouge (and the M2 scraper I turned into an NRS recently) not only seem to lose their sharpness in a matter of minutes, but the edges also seem to literally deform. With the gouge, in less than 5 minutes most of the time, the nose goes from being a slightly rounded point (according to Batty's sharpening method) to a notched point with the notch offcenter according to the side of teh tool I've been using most. The wings will also deform a bit as well, although it takes longer. Once I notice this, I re-sharpen, but, I am honestly wondering if there is actually something wrong with this gouge. I've tried to avoid any bluing, and if I get any, I lighten my touch and keep grinding until the bluing is gone. I usually get a slight bit on the corners of the wings no matter what I do, but I don't really use those corners much. The rest of the gouge, as far as I can tell, has no bluing, but, I am wondering if having encountered that previously, if it still degraded the metal even in parts that weren't actually showing the issue? In any case, that gouge cuts REALLY well when its initially sharp, and I can get long sweeping cuts without tearout at all, which is one of the promises of the 40/40 grind. I think some of the minor tearout I do encounter, may be due to the rapid loss of the sharp edge... In any case, it works well, but, it requires resharpening constantly to keep it working well. Once I have the funds, a larger 40/40 grind in a better steel, is near the top of my list. The M42 steel does seem to hold its edge and its shape, well more than 10x longer than the HSS gouge does.
I missed this months meeting, but, I plan to start going to the front range woodturners meetings which are near the beginning of each month. Who knows, maybe I'll be able to meet someone at one of these who would be willing to take a look at my turning and give me some pointers. I think, its probably sanding technique, though, I think my actual turning with tools is ok. I still have some perfecting to to, in terms of following the curve as I cut, and cutting in continuous cuts (sometimes I still cut past the wood and have to back up and re-start a new cut), and learning how to use scrapers to optimal effect (I am fairly good with NRS on the inside of bowls, but I still occasionally bite the wood so I'm sure there are technique improvements I could make.) Overall though, I don't think its the tooling leaving the scratches (especially since most of the time, the scratches are usually perpendicular to the orientation of tooling marks.)
I need to find some harder woods, to try turning bowls/platters out of, and see if I still encounter the scratch problem. Maybe it is a softer wood issue, and maybe it is due to damaged fibers deeper into the wood. The holly really seems to have issues. Maple often does, and Cherry. I think all of the woods I can remember this happening most with, are under Janka 1400? I think holly is around 1000.