With regards to theme resources - it's not moving the files (mostly - images are moved), but it's actually just re-creating them on the fly from what's in the database as you access the site.
When it does this, it automatically creates the folder using PHP's mkdir() function and attempts to CHMOD it to the correct permissions using the chmod() function. If either of those fail, then an error will be thrown. Both of these do, use the configurations as noted in the documentation.
It will only ever do this once, though, when it creates the folder. If the CHMOD permissions of the folder are being changed after it was initially created, then that would be caused by something else outside of the software. I'm not seeing any instances where the software changes it to a value other than what is defined by your configuration.
All of that said, however, getting to the root cause of this would likely require us to take a look at the affected site. If you are still experiencing this issue, I would recommend starting your own topic so we can start clean and take a look for you specifically.