Since there was no reply from the plugin author and it appears that he has no intention of fixing this, I wrote a cron script that scans the directories I need pushed to the cdn and it generates a list and pushes files every 5 minutes. Not a perfect fix but it works.
On another note, the problem seems to be related to the number of files in the uploads and gallery directories, in my case there was well over 600K files.
Another avenue you could pursue is to push all the files to the cdn and then cleanup /archive the uploads and gallery directories and move it offline.
