I've used BackPack with no problem on my demo site but on the working site when I try to run a full database backup it begins downloading an index.php file instead of the backup file (It works fine for optimizing and module backups). It will backup when I select Table Structure only but if I select Table Data, it starts a download of index.php. Same thing happens under the Table Backup tab. Does anyone have any idea why this would happen? Could it be the version of MySQL?

Disregard. I am using the XOOPS2 backup module as it works just fine.

According to the changelog of BackPack, version 0.83 should work with MySql versions under 4.0.2.

You can try BackPack 0.84 which is available here.