I finally have an apparent cause of this problem, and a somewhat solution.
The problem is caused by this bug:
http://bugzilla.scalix.com/show_bug.cgi?id=12624 . Basically, under several sets of circumstances, pending deletes are not cleaned up, so when omoff is used to shut down imap and rci, the containers are left open and the processes are killed while there are still pending deletes. This causes the mailstore to become corrupt, producing either a "Bad magic number in header" error or "Current container has not been upgraded to current format" error. I have been told that this bug is fixed in v11.
The solution: don't use omoff. I converted my server to use LVM and do a snapshot backup to another server. On the other server, I bring up Scalix and do individual omcpoutu's for each user. This works great, as long as you have an up to date version of RedHat (or any other distribution). If you are using RHEL, you *MUST* have at least "Nahant Update 3" or later. I don't know what you need for other distributions. The problem with older releases is that there was a bug in the devmapper code that would crash the system when using an LVM snapshot (
http://www.scalix.com/community/viewtop ... hlight=lvm).
I could have just waited until v11 becomes available, but I chose to go down the LVM path for the simple reason that not only does it give me a backup solution, but it also gives me a warm-spare server should anything happen to my main server.