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ran into similar troubles with SS 2.3.2 RC2.
Modifications from http://silverstripe.org/general-questions/show/255947 are not useful here.
valid_elemnts are set to *
Did you edit the rewrites in tiny_mce_improvements.js ? Because these will strip your JS code...
How does your entered code look like, what does TinyMCE do with it?
I commented the rewrites from http://silverstripe.org/general-questions/show/255947 out.
But I still can`t insert <script> areas via the Html-Popup in TinyMCE.
As a test I inserted an alert statement (the one you gave cob-web), but it is still parsed out.
BTW: the function sapphiremce_cleanup in tiny_mce_improvements.js is called before the popup opens, after you close it and every time you move to or away from the page.
[Edit]If I inspect the page content in phpMyAdmin, the <script> tags are already removed. So it must be a TinyMCE .js script.