Since this problem still exists, and I don't have a clear path to figuring out what is causing it it isn't resolved in my case.
You mentioned a diagnostic version of this plugin that would identify what is causing this problem?
How can I go about getting that? I searched a bit but didn't find it right away.
I posted everything with 'wordpress' in it in the other thread but fail to understand how those would cause an entire directory to be not to be backed up?