It seems to be software related though since it works fine when not using the XInput option. I just tried in Goldeneye, and when you aim (holding down the R button) and move the analog stick the deadzone is noticeable while without XInput I can get much better precision.

Would there be any interest in adding the configurable deadzones for triggers/analog sticks feature request? It's one of the features I really miss when using Project64 in comparison to mupen64plus.