These are some of the issues I’ve had trying to backup with BackupBuddy. Perhaps you can learn from my mistakes.
1) BackupBuddy gets stuck zipping files I had successfully backed up a client’s site several times in the past, and then suddenly, the site wouldn’t finish the backup process and kept timing out. I noticed that the backup file size was much bigger than it had been in the past, but wasn’t sure why. Support suggested that I should check the size of the site in BackupBuddy’s Server Tools page -> Site Size Maps tab -> Display Directory Size Listing button. That button will show the total size of the site and where space is being used up (all with and without backup exclusions taken into account) and that can help see if there is any extra space being used (since you also mentioned the site being larger than expected from before).
Sure enough, I found that the client had uploaded a huge number of files that were making the site size too big for the backup. Then I went to BackupBuddy > Settings and excluded that particular folder at the bottom, and the site backed up fine.
Support also suggested I could try disabling zip compression in BackupBuddy’s Advanced Settings page to speed up zip file generation and check with the host on increasing max PHP runtime to give it longer to run (max_execution_time).
I’m going to add more things to this post as I run into them.