From the X4U mailing list, it appears there's a bug in mail.app in 10.1 that only affects some users who run mail.app with no rules enabled. In some circumstances, mail.app will not delete the messages on the server, leading to repetitive downloads of the same email over and over (even those that have been deleted and emptied from the trash). Cricket (an Apple software engineer) writes to the list with the solution:
"Do you have any Mail rules set up? If not, delete your MessageSorting.plist (from ~/Library/Mail) and restart Mail. That should take care of the problem, which should only affect some POP users that have no rules set up. We plan to fix this in a Software Update."
"Do you have any Mail rules set up? If not, delete your MessageSorting.plist (from ~/Library/Mail) and restart Mail. That should take care of the problem, which should only affect some POP users that have no rules set up. We plan to fix this in a Software Update."
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