I had the same issue, it's this:
in the latest evo packages for dapper, there's a bug that makes
"evolution -> mail preferences -> Junk -> include remote tests" behave
badly.
previously it didn't do anything, but now it marks all incoming mail as
junk, and hides it for some reason. all your email will be hidden until
you uncheck the box and restart evo. your hidden mail will be visible in
the junk folder.
the checkbox dos seem to do something when the right tools are installed
(spamassasin, bogofilter, I don't know?), but noone knows what exactely.
so general conclusion: don't check the "evolution -> mail preferences ->
Junk -> include remote tests" box. junk filtering in evo is horrible
anyway, unchecking it won't make it any worse ;-)
** Changed in: evolution (Ubuntu)
Status: Unconfirmed => Confirmed
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Missing emails in data file
https://launchpad.net/bugs/37858
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