I think I found an answer to the disappearing mail. This particular machine is not my primary mail machine. When setting up TB3 after the fresh 2010 install I let TB do it's autoconfig thing that seems to be built in now. It auto-magically sets the servers etc now. When it did that, it configured my email account as IMAP
instead of POP. My account is POP. I couldn't seem to find the "leave a copy on the server" checkbox but there was something similar in one of the account config dialog tabs. Guess it was not the same. Now that I have deleted my old account and reinstalled it while MANUALLY choosing POP instead of letting TB chose IMAP, I think the issue is resolved. So far I have not seen disappearing emails. So far......
Sometimes automation, and blind trust in it, can getcha.
I'll test for 24 hours and then mark "Solved".