GoDaddy web hosting causes BackupBuddy to balk at later stages of a complete backup, and I’ve been struggling with getting BB to run on different hosting spaces at GoDaddy. At last I found a good writeup which described how to configure BackupBuddy to work acceptably on GoDaddy hosting.
It only takes a few seconds to apply these tweaks to the BackupBuddy configuration in your WordPress admin panel. Backups take a little longer than on other hosting, but they do finish. If your backups always timeout incomplete then give these settings a try.