If you can understand what squiff has just said then I hope it helps
if not there's quite a bit of info on the net about scanning negatives like this one
http://www.cam.org/~qfhs/srch_scanning1.html or try this link for more google results
http://www.google.co.uk/search?hl=en...G=Search&meta=
I've never used a negative scanner so can't be much more help, hope you sort your problem