You say,
all messages in
one pop account get duplicated, correct. Does this always happen?
I'd try to find out, if the messages are really duplicates or if it is only Mail.app not showing them correctly.
To do this, count the messages in the respective INBOX, then go to
/Users/
_yourhomefolder__/Library/Mail/POP__the_account_in_question_/INBOX.mbox/Messages/
IF the duplicates are real, the number of the files in this folder should match your count in Mail.app exactly.
If there's only (but exactly) half of the files, we'd know that it is only Mail.app not showing the correct number of mails there are. This would lead me to assume you might have a problem with with the so called "Envelope Index".
I say "you might" – I'm sorry I can't give you a definite answer.
If the Envelope Index causes problems,
this entry on hawkwings.net might be of some help to you.
Please make sure you have a backup copy of your Mail folder and follow the instructions exactly.
--gregor