Hi
I have resolved this issue (for the time being at least) by uninstalling backwpup and then reinstalling.
I also deleted all of the repeated folders on my server.
Program somehow copies the main folder into itself the again and again, about 20 in my case. backwpup then starts looking in those folders and hits the problem.
Just keep checking the directory structure on your server.
hope one of the developers looks into this problem