Let me give you some background, and described what happened. I assume I'm kind of a unique case here, which is causing all kinds of your problems with your client.

Some suggestions. I would like my new messages on top. I assume sorting is on the "todo" list.
How do I delete a folder? I don't see an option.
Now for my problems...
My inbox has over 400 messages. Yes, I should clean it up.

I am running Dovecot on my Linux box. Connections seems to have no problems. When I first entered my information, the previous 1-2 weeks worth of mail started to download. All messages were marked as "new" (eventhough they are not new on the server.)
When I turned on sync, it started to download all 400+ messages. After about 150 messages, my Treo rebooted. After I restarted, I noticed that my messages were are "new", so I turned on the sync flag option. More syncing and the 150 messages were marked read (as they are on the server.) (IMHO, sync flags should be on by default.)
Anyway, I'm not sure what I did next. I believe I exited the program, but then came back to it. Currently I have only 30 messages in my inbox. They all have the wrong date. They are all the same (incorrect) date. These 30 messages are actually the first messages of my 400+ (from 2+ years ago.) I can't see my latest messages in my Inbox.
I have received new messages since this time, and they seem to be added correctly.
I'll play with it some more and report any more issues.