Maybe it is something totally different. What I see is at the moment is that it works ok in my English blog, but not in my Swedish. Both are using latest version of WP and plugins, though the Swedish blog use some additional plugins.
I have tried to deactivate all plugins (except MCE Table Buttons), but that did not help.
Actually there is one more problem (that I perhaps did not notice before or maybe it was not there then): The are no “tabs” that let me choose between “Visual” and “HTML” when editing a new post.
So something is rather seriously broken (if I am not totally missing something). At the moment I suspect the plugin “Raw HTML capability” or some interaction with this and another plugin, maybe this one since you are doing things in similar areas so to say.