I'll give your script a try this weekend.  In my infinite ignorance, I think something's going on with the Innodb engine.  There's a lot of info around on dbase corruption if Innodb is not shut down properly, etc.  I tried deleting the ibdata files and letting Maria recreate them when it came back up and I couldn't get it working, but I would always get different results depending on what I altered.  It's almost like whatever is shipped is different than whatever the installation creates and Maria doesn't like it.  Crazy stuff man.  :)