Hi Leo,
Yes, sounds like a bug in TinyMCE. I can't fix bugs in TinyMCE so if you have an older version on disk that works that is a good solution.
Another workaround is to use CKeditor in those cases where you need to add javascript into the content and then change back to TinyMCE for other editing.
Hopefully it will be fixed in the next version of TinyMCE.
Best,
Joe