Hmm, strange. Does the main control, presumably used to place the health/lifebar in the top left corner of the screen, have a mouse filter set to ignore/pass? Maybe it is covering the whole thing and that is causing the UI to not work.
Another thing to try is making the pause menu, but not actually pausing the game. This can help narrow down if pausing the game itself is causing the issue. If it works when the game is not paused, then it is likely something with the process mode that is causing the issue, while if it does not, then it is likely something with the UI setup.