Every scan program does that, IF you have color/exposure correction turned on. It's showing you a preview of what the results of the correction are going to be. An extreme example: a very yellowed and color-casted print on a flatbed scanner. When you do a preview that includes the stark white background of the scanner lid, it color corrects to that as white (i.e. no real color correction needed), but when you neck the marquee down to just the print area, then it refigures the color correction based on that and cleans up the images (and completely blows out the whites of the scanner lid, which you don't care about.) As you move the marquee from image to image of a previewed set, it's similarly refiguring its color correction values.
If there is a difference between what you see in the preview and what you see in the resulting scan, it's either because of the weirdness of the tiny size of the preview versus the full scan, or because you have color corrections turned on for previews but not for scans, or something like that (I use VueScan, not Silverfast, so I can't say for sure in your case.)
But in any event, clearly you should print these optically to avoid all this, as has been mentioned
Duncan