Debug log please, with "raw session data" enabled (see below).
In the log, please 1) check mail in the account 2) move a message or two to Deleted 3) empty deleted, let it finish sync 4) check mail again.
I can assume that the server returns inconsistent message IDs between "UIDL n" (one message) and "UIDL" (all messages). Just like Cyrus POP3 does. If the log confirms this, I'll add a workaround -- same as I've done for Cyrus.