I have the same controller - works great without any issues. I use the second analog stick for the yellow C-buttons - sweet.
The problems you are experiencing are more likely related to the games requiring a Controller Pak, which in the N64 world is a memory pack inserted in the controller. If you have your controller configured for a rumble pack instead, games that require the controller pak memory will either allow you to continue without saving or not work at all.
In order to male these games work, go into the nrage controller plugin and select a controller pak instead of rumble pak.
op