They probably can't be repaired because they are not InnoDB.
To answer your original question, like other people have said, MCC doesn't use the .htaccess at all. Can you see your .htaccess file? If so, what does it look like?
But chances are it's bare bones and probably just has some error pages defined if there is an error and your server admin doesn't really know what he's talking about. Because if you can reload he page and get it working 1 out of 100 times, chances are it's not your htaccess file