Did you upgrade recently? And did CUPS change from version 1.5.3 to 1.6.1 on your machine when you upgraded? The reason I ask is that there is a bug in CUPS 1.6.1 that affects some USB printers (like my Canon MP560, for example) and results in only part of a page being printed out. It is due to the new CUPS USB backend that was introduced in CUPS 1.5.4, and seems to affect quite a few Canon models, as well as some models of other printer manufacturers. I'm lucky in that my Canon printer supports both USB and WiFi connections, so my work-around is to print via WiFi instead of USB. See my post in the Gentoo Forums
with more details, including a link to the CUPS Bugzilla bug report. Hopefully it will be fixed in CUPS 1.7.