Solved this one on my own. It seems that Apple has neglected to update the Portable Home Directories syncing exclusion rules for the locations of the new Mail files, they still show the old Snow Leopard Locations.
In Worgroup Manager in mobility settings for the clients, under "Preference Sync" change the two Mail related items in the "Skip items..." section to the following:
Partial Path: ~/Library/Mail/V2/MailData/AvailableFeeds
Partial Path: ~/Library/Mail/V2/MailData/Envelope Index
(note the change from Full Path to Partial Path)
It really would be good if Apple did a little more QA before releasing their products.
Just wondering, what is the difference between "Partial Path" and "Full Path"?
I tried your solution but unfortunately does not work.
I have an IMAP account - which is excluded by default Lion Server rules - and a disabled POP account. Everytime I sync between 2 computers I have the problem.
Is it still working on your side?