At first I thought it was my imagination, but here's what happens:
I open Mail
Check Email
Emails get downloaded, and by default I'm in the Inbox (general/global inbox)
If there is an email thread, it will appear in the inbox, as it should.
if I click on an email that is threaded, I can view it, however if I then go to a folder within Mail, it says there are no emails in the folders (all of them), even though I have emails.
At that point, if I try and quit Mail, it freezes, and I then have to Force Quit it.
One point to note, I do not have the "organize by thread" option NOT checked.
I'm getting closer and closer to just doing a format, and have no desire to do so.... but these problems are getting to the point of annoyance.