I have exclusively used 5.0 on my machine for all my mail needs, using POP3, since 12/2. Until now 'delete from POP server' was turned off, but as of today has been switched on. As a consequence I got all ~2500 messages once again downloaded to my machine, even though Mail 5 should have preserved the 'watermark' of previosly downloaded messages.
Reassign to jefft. Need to address this before b1
Hmm.. this shouldn't happen.
This is fixed along fixing bug 22129. We failed to generate X-UIDL: header for each pop3 message when leave on server. Unfortunately, we cannot retrofit previous messages what have been downloaded. So, you might still get duplicate messages one more time. If you start with a new profile you shouldn't have this problem.
I tested the POP server on all platforms using 2000-05-01 and with pref to delete msgs from server checked and unchecked. Messages that were deleted locally as well as the server were not retrieved again in the same profile or a newly created profile. Verified. Please reopen if you find another scenario.