When we download an archive to do a manual deployment, the pair of files in the root directory are also duplicated in two sub-folders, the PR subfolder and the BL subfolder.Why is this the case?

Does your rule with the order of 20 (which is firing late) have a custom code action? I am seeing that custom code actions appear to execute somewhat asynchronously and cause rules to fire out of order, I'm wondering if you are seeing the same thing.