I found the problem. Enabling the option "Automatically check for new mails every X minutes" makes that account check for new mail on startup too. The description string should let the user know this, but it's not really a bug, it's just a wrong description, so I'm closing this report.
** Changed in: evolution (Ubuntu) Status: Unconfirmed => Fix Released -- fetching mail at startup doesn't fetch all mail https://launchpad.net/bugs/51222 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs