Apologies for having left this so long unanswered. I bought my scanner new when it was still current (walked out of the B&H store in NYC with the last one they had in stock). Used it to scan 400-odd slides, then life intervened in various ways and the scanner sat unused for years. Now it needs at least cleaning, and perhaps an overhaul. I will have more to relate when I get it back from the overhaul.
All the slides I did scan back then were Kodachrome (mostly K25, some K64). Some of them shot under harsh sunlight conditions in the Saudi Arabian desert. I was able to get very satisfactory scans but in a few cases had to do a bit of tinkering in the Nikon software. At one point we were camped in a red sand district and the color of the sand (in the slides) changed dramatically as the light changed at different times of day. I was photographing falconry action, bucketing across rough ground at 80 mph in a Range Rover with 4 cameras strapped on, a different lens on each (falconry action is far, fast and furious and there's no time to change lenses). I was also doing the driving, the action is so fast and furious there's no time to explain to a second person where you need to be at each moment. After three months of that the cameras looked quite battered - but Nikon AG in Switzerland restored them to as-new condition, I don't know how.
In a few cases I recorded the scanning tweaks in the name of the resulting scanned image. Here are a couple of samples:
"My tent 34B04 with DEE, shadow 75, gamma +2.20 full auto adjust crop" (the best of 6 scans with different tweaks)
"My tent 34B09 with DEE, shadow 75, ICE crop" (best of 3 scans)
These are two shots of my tent, with me in front of it in full Arab dress, taken at different times on the same day, requiring somewhat different tweaks to make the sand color even approximately match. Actually to make the rest of the picture (tent, falcons, myself, etc.) approximately match - the sand color still looks different in the two shots -- taken maybe half an hour apart in the late afternoon, when light conditions change very rapidly.
These are 35mm Kodachrome slides, scanned at 4000 dpi, giving images only slightly smaller in pixel count (5782 x 3946) than the digital images I now shoot (6016 x 4016) with a Nikon D600 digital SLR. Not much difference in image quality either. Fine for at least 16" x 20" salon-quality enlargements.
Actually those two were the most troublesome of the 421 scans (only a few sets of multiples) of my Saudi Arabian material (only about 35,000 still left to do). Nearly all of them came out well on the first pass.
So the short answer is no, I did not experience that kind of problem - but I also did not expect everything to come out "correct" (whatever that is) without a bit of tinkering. It may also be relevant that all my originals were Kodachrome. Kodachrome has its own distinctive characteristics, and other slide films may behave somewhat differently when it comes to being scanned.
When I get my scanner back, and tackle a wider range of subject matter, I may well have more to say on this topic. I do not consider myself any kind of expert on slide scanning.