Matt, I can confirm something else is going on with comox.
I tested and all the methods of copy/paste tags work as they should, with the appropriate dialogs appearing in the appropriate circumstances.
Comox, I wonder if you are running some nifty clipboard manager utility in the background. Please check. I also wonder if you have a sticky shift or ctrl key; this can happen because of Windows accessibility settings, and mouse software (logitech sometimes does this).
I also suggest rebooting your computer, and if the problem persists, post a video showing your last example. Because doing a copy/paste to the same file in MC is illegal and throws a dialog box complaining about it, which you claim is not happening.