The holders just hold the neg in place, I can't image it would affect color
They also hold the negs away from the all-important first centimetre of the glass, which the scanner uses to calibrate itself when in transparency mode. Put *anything* in this region and it's anybody's guess how the scan will come out. (See http://www.elvum.net/gallery/holga/police_trafalfar_square_bad_scan for just one example; overall casts are perfectly possible too...)
S
