Hey lazy_breeze, I just signed up to tell you that I MAY have found a solution.
I was having the same problem as you were having, but I found that the L & R triggers were the culprit.
So assuming that you’re using that Wii U GCN Adapter software (the one that uses vJoy), what I did was:
A) Go to configuration and adjust the deadzones for L/R-triggers to 90%, then save and close.
B) Go to Windows Gampad Info, then click properties, and then calibrate the stick.
This took me an hour to figure it out, but not only did I fix the input problem, I also calibrated the control stick to go all the way.