I've just seen something similar to this. After an upgrade all messages were being marked as junk, I did not have remote tests enabled.
Curiously, disabling junk tests and the reenabling them seems to have fixed the problem. However I still see this in the log: concordia ~$ evolution CalDAV Eplugin starting up ... (evolution-2.6:20176): evolution-mail-WARNING **: ignored this junk plugin: not enabled or we have already loaded one (evolution-2.6:20176): e-utils-WARNING **: Plugin 'Spamassassin junk plugin' failed to load hook 'org.gnome.evolution.mail.junk:1.0' -- Missing emails in data file https://launchpad.net/bugs/37858 -- desktop-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/desktop-bugs
