I just finished editing a Rich Media unit in Flash CC. The FLA contained a MovieClip that had a frame script that I needed to make a few edits to. Unfortunately FlashCC did not save these changes when I saved the file. When I opened the file again it had completely reverted to the origional version. I made a few changes again just to test, and was still unable to save the changes. Finally I opened the FLA in CS6 and finished the project successfully.
I remeber a similar bug when they introduced the ability to "Pin" frame scripts - changes made to the pinned scripts did not save. I wonder if this is something similar in relation to the new script sidebar.
In any case, be warned that your scripts may not save!
For the record, this FLA was created in CS6.
If the problem is reproducible with a fla then can you please share the same? It'll help us debug the issue.