Have you tried manually deleting those old directories and then seeing if Comet Cache works the way it's supposed to?
Yes, I deleted them with no issues but now the cache dir is, once again, full of empty dirs that never get deleted.
When I click the "Clear Cache" button, the 'deleteFilesFromCacheDir' function always breaks at the point I indicated, so the dir does not get deleted. So the issue is not related to permissions of the dirs... but related to the script never attempting to delete those dirs.
Right now there are 4605 dirs and 844 files at /cache/comet-cache/cache/http/www-mysite-com. Some of the dirs are two days old (I deleted all empty dirs two days ago), while files are less than 3 hours old (max age=2 hours and cleanup process=hourly)