This is getting seriously wierd... never heard of anything like this before.
You have completely replaced the editor folder and have not seen any change? When you went in did you get the update process via the Notifications page? Removing the editor should have undone any configuration change They finally dumped HTMLarea but Plain area should be useful for writing simple text, if nothing else, but even so, replacing the editors should resolve the problems.
Have you looked at the TinyMCE web site for any alerts? There can be things in an environment that impact on TinyMCE. That is, really, the only other thing, if there is nothing inside Moodle, then it has to be outside - something in the environment.
Sorry I can't be any more help, but you really need an expert in TinyMCE/Moodle integration.
You may also want to put this into Moodle Tracker, the Devs spend more time there than they do here I think. At least have have a better chance of directly contacting a Dev who can help than here.