Here at the NCMI we're running two Nikon 9000 scanners on two Windows machines. We have modified the holders (FH-869M) in-house so that the film is sandwiched between two sheets of anti-Newton glass. We also found that the film holders/scanning system had a slight downward tilt from SW the NE (looking from above the machine).

The bottom piece of glass is glued to the film holder, on which the film is placed, and then the top sheet of glass is placed on top by the Nikon scanner operator. The top piece of glass and film are held roughly in place by make-shift guides. Important points are

The glass didn't come with the holder we had to order it in. Because the bottom piece of glass is glued it stays there, but the sandwiching piece just slides around unless you think of someway to hold it still - so we just put some bits of thick tape here and there so everything stays approximately still. We had to shave some plastic from the bottom too, just using a pocket knife. It's a bit of a hack but it works fine.

I will add some pictures shortly.