I have a Canon tech coming out tommorrow to have a look. Hopefully he can offer some help. I have seen the problem on two separate ipf5000's so I dont think it is a fault with my printer.
I actually found there is a test pattern for calibrating the feed in the trailing edge, this however did not seem to help.
Personally I think it is a software bug as it goes wrong about 1 inch from the end of the paper, and comes right about 1/2 inch before the end of the paper.
Anyone else seen this ?