I don't have a bonafide answer for you, but I do have some questions or suggestions to try.
1. Are you running the backup as an admin? This would be difficult to do on a schedule as you wouldn't be able to right click and choose "Run as"
2. Is the computer you are running it on an administrator or if on a domain, are you logged in as the admin?
3. Are you backing up over the network?
4. Are you backing up offsite?
5. How many locations are you backing up to?
6. Do you have "Check database for errors before each backup?" If no, check it. More importantly, if yes, uncheck it.
7. Are you including imported items? If so, exclude them.
8. Do you have "Check encrypted file for errors when finished?" If no, check it, if yes, uncheck it.
9. Do you have "Check Zip file for errors when finished?" If no, check it, if yes, uncheck it.
Personally, I choose not to run the AC backup on a scheduler. For me, it is just as easy to just have the shortcut on my desktop and click it before I go. Given I don't back up the imported items, it takes about two minutes. During this same time I am backing up my files/imported items and my billing database. I can then see that it is done properly. Maybe it would be helpful to at least do this for a few days and see when and where the error occurs. It may be that you have some errors or corrupted files in your database. Try running Amazing Utilities and optimizing the database. Try fixing a corrupted database in AU. If there are errors and you have the "Check for errors" checked, this may be your issue.
Other than that, ping support and see if they have a fix.
