<font color=red><font size="5">UPDATE 2 - Problem resolved!</font></font>
Well, it turns out that the bug I thought I had was nothing but a red herring. I'm a bit embarrassed to say that I missed converting a function call to a namespace call in some code I was converting, and erroneously assumed that the plugin was at fault.
I now am quite sure that the plugin is working as intended!
I've nonetheless updated the plugin download link to an new version of the plugin. The major change of note is that individual namespace objects now maintain their own function stacks. This will probably prevent weird collisions with nested namespace calls.
I've also updated the demo to be much more extensive and easier to read. Be sure to clear your browser cache if you've looked at it before.