I've been a bit flooded with work and was just about to reply to your PM. Make sure that patches are empty before starting the script, if those particular patches have not been filled by the script itself. The script uses caching to remember what will be done at which location(s), but for that you need to use the same profile. The script does not know anything about patches that are filled by yourself and not the script.
Please do let me know if this did not answer your question(s)/fixes your issue(s).