I have a genuine N64 grey controller, and the Boom PSX/N64 USB adapter.
After calibrating the controller in WinXP Control Panel, I tried to set the controller in PJ64 Controller Options. I was using the default "Jabo's DirectInput7 1.6" as the controller plugin. When trying to set the analogue stick controls, PJ64 seemed to get very confused and reported me pushing the stick left as "Zr+" or suchlike.
Then I switched to "N-Rages's Direct-Input8 V2 1.80a" plugin. This plugin correctly recognised me pushing the stick left as "X-" (or suchlike). I set the deadzone to 0%, and my N64 emulation works a treat!! 100 times better than the original console!!!