Aha! I have had this bug too but...

I have just found that Evo is independently classifying some messages as
junk and storing them in the Junk folder. In Thuinderbird they still
show up in the inbox but in Evo they don't appear in the Inbox!

This may be because of the Spamassassin plugin.

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Some emails are not displayed but are saved in the mailbox file
https://bugs.launchpad.net/bugs/247364
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