ModSecurity in my server was causing issues. BPS Pro was not able to save custom htaccess. and several other features were not working.
ModSecurity was seeing some features as an injection and I was getting 500 & 403 errors. I had to whitelist several rules.
And presently still have to whitelist rules because of updates to modsec rules.
I also have Backup Buddy working. It works by using CPanels Backup utilities. Yes, you just paid for the convenience of doing a backup from wordpress that can be done in cpanel. =)
Anyhow, its worth having a look at the logs for ModSec. In putty/cmd line run the following:
grep YOURDOMAINNAME.com /usr/local/apache/logs/error_log | grep ModSecurity
Look at the Putty command above, replace your domain name and verify that the path to your error log is the same, or else change it to your path. The command “grep” will display modsecurity logs. Its like a filter.
So now run a Backup Buddy Backup and then run the command and see if you notice a time match, the same day and time. If you find something then post the error.