I thought I read someplace (probably here) that new IPF5000's were shipping with a different firmware release.
Yes, the current ones are being delivered with 1.12 or 1.13 (mine had 1.08 when I got it). However, none of the known bugs were fixed with this firmware version. I know, because I loaded it, along with the plugin and driver updates from Canon Europe.
We only have translated Japanese to go by (since Canon USA has not seen fit to put the firmware on their site, although it was released by Canon Japan one month ago) so it is hard to tell what has changed. The most significant change seems to be a new menu option on the printer LCD menu called added "TrimEdge Reload". We believe it either just trims the edge to make it square, or trims off the printed barcode (not sure which) when paper is reloaded.
The most troublesome bug is banding in the trailing inch of images printed from the Cassette. While subtle, I noticed it immediately when I printed. This is mainly a problem with letter size paper, since larger sheets are likely to have a one inch margin so the problem will not be manifested. Some people say they don't have the banding, but my guess is that they just aren't looking at the right kind of image to see it. To that end, I have created a Banding Test File so there is a standard file used for testing. Referenced in this thread on the IPF5000 Wiki:
http://canonipf5000.wikispaces.com/message/view/FAQ/231558Anyone who wants to test a file known to produce banding (on my printer anyway :-) can download the file and run the test. Exact directions are included so that any possible variables which might affect the result are standardized. Please only download the file if you plan to test and report back, since the bandwidth of the web site I put the file on is limited to 20 GB per month (file is 50 MB zip).
--John