configure the backend init script to log autoexpires:
near the top, add --printexpire to the "ARGS=" line, so it looks like this:
$ sudo nano /etc/init.d/mythtv-backend
that should log the deletions, if the backend is autoexpiring your recordings.
ARGS="--daemon --logfile /var/log/mythtv/mythbackend.log --pidfile $RUNDIR/$NAME.pid --printexpire"
in the meantime, i recommend installing phpmyadmin to see if tables need repairing:
if there are tabes that need repaired, make sure to go back and double-check the autoexpire settings in frontend setup after the repair.
also, make sure you have the MYSQL optimization options set in mythbuntu control centre advanced settings.
if all else fails, you can always add --noautoexpire to the ARGS list in the init script, which will prevent the autoexpire thread from being launched. if you do this, you will need to manually delete any unwanted recordings including livetv recordings.