Time Machine does not create ACLs - Access Control Lists - in its backups. Instead it adds "extended attributes" to each file and folder, which is something different. If you restore these files by hand, by copying them straight onto your hard drive, the extended attributes are carried along and will prevent you from altering the files later.
To remove the attributes that Time Machine creates, these two commands will work:
find . -print0 | xargs -0 xattr -d com.apple.metadata:_kTimeMachineOldestSnapshot find . -print0 | xargs -0 xattr -d com.apple.metadata:_kTimeMachineNewestSnapshot
Run them as root, and at the base of the tree you want to clear.