Yes, I have been having the same problem. I just set up my email last night, too!
ya, the email app is crap, I have all but stopped using it. Whenever I hit the sync button it will remove most of my messages then I need to hit sync again and it might or might not load my new messages.
Also the new email notification is spotty at best. Sometimes it tells me, mostly it doesn't. I am setup with IMAP and it should sync much more smoothly, ahh well, there's always rooting I guess...