it could be that in calks SYS every module contains the file that the module represents. try using an app called dump sorter to delete them. you can find dump sorter here:
http://forum.xda-developers.com/showthread.php?t=542081
I just discovered it last night, previously I was manually deleting the files inside the module directories. just check off delete files with the same name as their folders and point the app and the SYS folder. make a backup just in case. not sure if that will help but its always good to save space, every module on your HDD that is like that will take up twice the space.