Let's do a test.
Enter this into your console:
$mask="Add-Ons/*.zip";for($file=findFirstFile($mask);$file!$="";$file=findNextFile($mask))echo($file);
Then post the results. There should be a reverse-alphabetical list of all add-ons.
If the above fails, try it again, but first rename your Add-Ons folder to "Add-Ons OLD". This will cause all non-default mods to be removed.