OK, I don't use Vuescan very often, but according to Sascha Steinhoff, page 106 of his good book on this software, the application (presumably you are using the most recent version) is supposed to analyze the frame gap and use that information to align the image correctly. He says if for some reason it doesn't work automatically, you can turn that feature off and use a fairly simple procedure he describes for re-alignment. If that's what you mean by wasting time fiddling with alignment I see the point. I never ever used Nikon Scan so I have no idea whether it did this correctly all the time. However, as things stand at this juncture I think you have three options; from the looks of it, you may be choosing between the least-worst:
(1) Use Nikon Scan on your old computer and suffer the performance hit relative to current technology;
(2) Use Vuescan and take a risk of having to fiddle the periodic frame that doesn't align correctly on its own;
(3) Try SilverFast 8, which has a neat graphic frame alignment tool that works quickly, (you can download a free trial and see how you like it); unfortunately the Nikon version is rather costly, but a very nicely redesigned application.