I think the difference might be in the location of the rotor on the hub itself. I remember running into a similar problem when trying to run the stock 350X front hub/rotor on my 350X that has a 250r fork set up on it. It had me puzzled for a while and I ended up going back to the 250r front hub I think.
John
1985 Eddie Sanders ATC330r
1986 Monstecate
1984 ATC70 (awaiting 125cc transplant)
1984 ATC125M
1986 GSXR 750 - Keepin' it old school!
1999 Arctic Cat 500 4x4 plow machine
1999 Arctic Cat Thundercat 1000 (lake lizard)
1996 Arctic Cat Jag 440 L/C (ditch banger)