Am I correct in thinking that with the UIDL changing, the POP client will decide it doesn't know what messages have been downloaded and will download them all again? If that's the case, why is the UIDL from gamma different from the other two servers when each are logging in to the same account name and looking at the same exact files on the back end?
UIDL management changed in the 2.x series. When upgrading from 1.x, the existing UIDLs are preserved; but if you started with 2.1 and downgraded 1.x (which is essentially what you did, in your little experiment), the 1.x POP3 server did not understand 2.1's UIDLs, and assigned its own UIDLs.
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