I wanted to send along a follow up note. After upgrading to the latest MySQL, I recompiled PHP and all of the associated files with it by doing a ./build php_ap2 y command and then following that up by building php perl, frontpage, and zend. I restarted httpd and that part worked fine.
However, immediately afterwards I noticed that email wasn't coming in. I didn't think anything of this and ignored it for about 2 hours. I started getting a few phone calls from clients about email not coming through and then I re-examined the issue and backtracked. I checked and email WAS being delievered into the mail files on the server. As I could log into directadmin and watch the size of a person's pop/imap account grow.
Then I began trying to login via webmail and roundcube, but each of those indicated that there was *no* email and that the inboxes were empty. I knew otherwise because I could see the virtual pop account sizes grow. At this point I stopped and restarted both exim and dovecot, but neither of those worked.
Finally at last moment thought, I decided to recompile and install dovecot because I was running RC31 rather than the final release. So I grabbed the final release, compiled it using the proper commands as given by DirectAdmin. Finally after doing that I restarted exim and dovecot, and sure enough it worked! I was able to immediately download emails from the pop accounts AND send emails.
The problem that existed was that even a client like outlook would time out when looking for the server, and would not be able to send or receive email. Here is where it got really weird. If I logged onto the server (before recompiling dovecot) and created a new pop3 account, I could send and receive email just fine. When I recompiled/installed dovecot... the problem was solved.
I have notified John about this to see what might be done or reported to the dev teams of both products.
Brad