This may be old news, but I just came across it on Canon's website while looking for something else. There is a known issue with Certain Canon DSLR;s and Lexar CF flash cards whereas images disappear from the card. Here is the link to the article, which also directs you to the firmware needed to correct the issue.
http://www.usa.canon.com/consumer/controller?act=PgComSmModDisplayAct&fcategoryid=215&modelid=11154&keycode=2112&id=27683
http://www.usa.canon.com/consumer/controller?act=PgComSmModDisplayAct&fcategoryid=215&modelid=11154&keycode=2112&id=27683