OK, so much for my theory then. Most of the files are not ones used by SQL or Oracle, so unless v11 has a much bigger list of known files which will always be in use it's not what I thought.
Do you still have access to your old backup server to compare the backup jobs? If you do, try having a look at the old one and going into the text view (since it's easier to see the list than with the GUI), and then see if the old job had a load of exclusions listed in it, in case someone had already gone through the job and excluded the folders which were always failing.
The other possibility is, did you have the AOFO installed on your old v10 installation, and if so have you not got it installed on this installation?