This seems like it could be a corruption in your original file. Could you try doing a FileMaker 11 recover of the file? Does it do the same thing?...that is mess up the script folders?
If so, I would try moving all the folders out of the scripts or doing a mass copy/paste of some of the affected scripts to see if they get cleaned up in the delete/and recreation. Just some ideas...
Helping businesses become more effective, productive, and profitable through custom iPad/iPhone applications, FileMaker app solutions, and web site design.