I have this problem intermittently with the Pre running 1.4.5 (or thereabouts, whatever Sprint has released.) I have it on both my POP3 account and on my gmail account. It has been less frequent since the latest system upgrade, and also became much less frequent when I changed the email service provider on the POP3 account. But I definitely get it on the gmail (imap) account from time to time, too.
I think it's some sort of memory management issue, and I had hoped it would go away with the Pre 2. Rebooting sometimes helps. It seems to work better when there's less email on the gadget, but I've never seen an immediate "fix" from deleting emails, perhaps because it takes a while for it to clear out registers or something.
This was the primary reason I used Classic for a while. (I had to get rid of Classic because the email files it stored internally were too large, and I got "too many cards" errors when I tried to open a single application.) With my prior provider, I sometimes resorted to looking at the web interface from my email provider. FWIW, that would often trigger the wayward post to "go through", but not always.
I desperately wish someone would write a good email application for the Pre. My ideal application would not only work more smoothly, but would give more explicit status messages (e.g. "downloading post 4 of 12 new posts")
The problems with email being slow and a little flaky to download were what drove my brother to an Epic. He doesn't like the Epic, but says at least all his phone calls and emails get through. (He switched from a Sprint Pre, so he was also on 1.4.5)