I haven't heard of this before. Some photos will help. What size frame and what size tires do you have?
I have a 17.5 inch Rockhound with 26 inch wheels. I ordered it in 2000 and I believe it was one of the earliest disc frames. I will try to email a pic (easier than posting here).
Basically the widest section of the q/r nut catches on the rear derailleur closest to the dropout while the q/r axle catches on the bottom forward face of the dropout. I tried a different q/r nut but is actually wider at its base. If it helps, it's a 952 XTR der and a Bontrager Race Disc q/r.
This isn't big deal, I was just curious if anyone has dealt with this. I considered putting a shadow rear derailleur to rectify this.