I am having issues also after Lion upgrade with my mail.
AOL and Gmail are fine, but my MS Exchange account is horrible. Account now appears twice, signature would not work (finally fixed by adding it to "both/duplicate" accounts") grouped messages do not appear as they should, or do in the other accounts, messages load slow. So far this aspect of Lion is terrible.
It also asks for my password multiple times.
I subscribe to the above problems. When I try to connect to the mail server at my job (IMAP) using SSL (993), the connection fails. However, when I am in the intranet and I switch to the non-SSL connection (available only from the inside on port 143), the connection succeeds.
Everything worked fine until I upgraded to Lion. And everything works fine on the iPhone / iPad.
I tried creating the account from scratch, even logged in as another user (I thought that maybe there were some caching / certificate problems). Still the same behaviour.
This is not an isolated problem. People in another thread have the same problem: <https://discussions.apple.com/thread/3188992?start=0&tstart=0>.
It seems IMAP/SSL sends a malformed authentication request in some cases. The problem seems
to go away if you don't use SSL.