We have had a problem recently with dovecot corrupting it’s index files.  I do not know exactly when this started.  The version that Ubuntu provides is 2.3.11.

     I recently changed the mail client server from keeping things on an NFS mounted partition to local disk as the general consensus within the dovecot community seemed to suggest this was a NFS related problem.

     However, that did not resolve the issue.  Today I compiled the most recent version, 2.4-devel and installed it.  I also changed the locking from fcntl to dotlock which is slower but generally considered more reliable.