Hi Jim Haney,
Thanks for submitting your post and for your info/video.
I haven't been able to reproduce the issue using newly created FileMaker Pro 11 files and older files I had at my disposal. in my converted files, the scripts will always remain where I place them in the list.
Maybe further background information might help us out. Does this behavior happen with all of your converted files? Or, instead of a new script in the 'problem' file can you recreate the issue in a sample file? If FileMaker 12 Recovery is run on the file, are any changes made to the database?