There is still some weird stuff on feeding from the top tray for some printers. Your problem sounds different than mine, but closely related. I can't feed from the top tray with the roll feed holder installed. Canon tech couldn't get it to work either, although he couldn't figure out WHY it wouldn't work. Canon tech support ordered some parts, tech will be back in a week to install them. They will definitely fix this sort of problem, so don't smash the IPF5000 just yet!
A couple of questions:
1) Have you loaded latest firmware (1.23) and software from Canon USA (assuming you are in U.S.)? You have to call Canon to get a CD sent to you (next business day), as the updates aren't on Canon USA web site yet.
2) Have you called Canon tech support? They are pretty good with these sorts of problems. You may need a visit from the tech.
Good luck, and let us know the outcome so we can add it to the Wiki FAQ.