Nikon still maintains basic troubleshooting documents for scanner hardware and software on its Support website. But as I suspected, they only go so far, and they can't troubleshoot issues that appear isolated to SilverFast or VueScan. My scanner passes all the nominal hardware tests (basically limited to making sure the green light blinks as expected when powering up with no other devices attached and the USB cord connected to the rear USB jack). My scan results from Nikon Scan are the same now as they were six years ago.
I opened a ticket with Nikon tech support and, after I told them my scanner was working properly with Nikon Scan, this was their final response:
As I think about this more, I guess I'm not convinced that my use of multi-sample scanning would be considered "overcompensation" for a hardware problem as you suggest. It would seem that multi-sample scanning is simply "compensating" for difficult circumstances. In other words, it's working as intended. I understand that in your experience you never needed more than 2x multi-sample scanning to produce acceptable results. But as this thread has suggested, you and I have different reactions to the same image. Recall that you didn't see jagged edges on my 100% images where the jagged edges were obvious to me. We have different monitors, different eyes, and perhaps different thresholds of acceptability.
Just to be accurate about this, at 300% we are seeing the same issues. At 100% we are not. I'm using an NEC PA271 at resolution of 2560*1440. with L calibrated at 100. Recall I examined your images in Photoshop in Screen Blend Mode to make sure I could see detail that may be otherwise smothered in darkness. When I wear my computer glasses my vision is very well corrected and I've been examining image detail in photographs over a time span of 50+ years, so I am quite confident that I know whato to look for and whether I am seeing properly. That doesn't mean I can't miss a trick or two, or that your problem isn't real - it is.
It is good that Nikon is willing to examine your scanner, but I understand your reluctance to send it in, because it really isn't clear yet whether the root cause of this problem is hardware or software. Even with no multisampling and no multiexposure you should not be getting those artifacts, so let us sweep that issue aside. I am inclined to think there could be a hardware issue simply because two different scanning applications are producing similar effects with the same unit. But if you are not experiencing this problem with Nikon Scan, that could mean there is something in Nikon's driver that controls the scanner in a manner that neither SilverFast nor Vuescan got right. So that would point back to software - see what I mean? Back to the drawing board.
I'm working on a good candidate image just now - has the kind of contrast that would show up such problems. The left side of the bottom image is the whole frame showing the small white rectangle that becomes the content at 300% display magnification, shown on the right side and larher in the upper image. The bright vertical material, being part of a window ledge and a drain pipe on the building wall do show vertical stripes. Not clear, however, whether these are display pixelation artifacts, or image artifacts. To assess that, one needs to print the image, so the display magnification is no longer in contention. I printed the 4000 PPI scan from LR4 on a US Letter size sheet in my Epson 4900 on gloss paper, and examined those sections under a 7x aspherical loupe. No artifacts showed.
Pushing this further, I downsized (not downsampled) the image to 180 PPI so I could make a letter size print of the area in the yellow box, then examined those same vertical brights using the 7x aspherical loupe, and guess what - those lines are there loud and clear as I see them on display; hence the issue not due to display pixelation. So correct me if I'm wrong, but I think I've now replicated your problem; to see it however, requires extreme kind of magnifications and close-up inspection that would seldom figure in most photographic work most people do, indicating that your requirements are quite exceptional, but of course no less real or legitimate. I think I've taken this as far as I can - i.e. I don't know the causes or how abnormal.