Apple Mail 5.3 seems to corrupt/lose its place in message id sequence numbers

OS/X 10.7/Apple mail 5.3 seems to corrupt (or at least lose its place in) the message id sequence number. Two days ago, around 2:0x mail stopped fetching email from a pop server that I own (all installed through WHM and CPanel at WestHost). This happened again today sometime around 2:0y.
Logging into webmail showed a number of emails pending. Bouncing mail or restarting OS/X yielded no joy.
When I delete the email account in Mail->Preferences->Accounts and then recreate it, it fetches all the mail as expected.
Any ideas on how to figure out what is going on?
Note that CPanel did undergo a big upgrade to 11.34 on Tuesday, so my initial thought was that was culprit, but since delete/recreate of the mail account fixes, I am not so sure.
thanks in advance,
Mike.

Forgot to add, no one else using this pop server reported any problems (and I checked).
Mike.

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