I'm being constantly frustrated with this issue, and I'm still not sure the best way to solve it.
I have my ubuntu server running headless with cgminer, and it is configured to automatically take security updates.
WHY is it configured to automatically take updates? You aren't running windows.
I think you have identified the source of your frustrations.
Turn off automatic updated. If it ain't broken, don't break it.
Not all updates, just security ones. The intent is to prevent the server from being compromised, however ubuntu "security only" updates aren't just security updates.