well, multiple times per day is a bit extreme.
Can't see why you may need this.
I guess you don't change your settings too often, so what changes multiple times per day is only the message bases.
I have theBat set to leave messages on server for 10 days, and I make a full backup of the mail folder every week (full backup means just Rar-ing the whole mail folder, a method much better, simpler and problem-free than using the built-in backup feature).
Now if something goes wrong, I can always restore the last backup and then get the missing messages from server.
If you need to backup your settings (without message bases)more often, just rar the mail folder excluding *.tbb and *.tbi files - this will result in a small (several kilobytes) backup file containing your settings only.
Rar backups can be easily scheduled with the Windows task scheduler.
(I use Winrar myself, but you can use any other archiver instead)