This is a very odd bug, which you may not be able to reproduce. I've got a bunch of accounts - two on my own IMAP server (atmail.ims.net), one on one university server (mail.physics.wisc.edu) and one on another university server (hokin.pobox.stanford.edu). All load messages fine but the last, which always drops the most recent message after it has been loaded the first time following a refresh. That is, I see it at the top, try to open it, and the message view closes out and the message is gone. After I refresh again, I can usually read it, although occasionally it happens once again and I have to refresh a third time.
I'm guessing this is a server-side bug, but I thought I'd report it. The IMAP settings are:
server: hokin.pobox.stanford.edu (custom host for every user)
port: 993
security type: SSL (strict check)
authentication: choose automatically
Not a massively horrible bug, but its been present since I got this Stanford account over a year ago.
Otherwise, I love Aquamail! Молодец!