7i92 & C11G BOB issues

I'm trying to setup my machine using pncconf but I'm running into issues.  I flashed mesa with the c11g bit file but when I use the auto discovery option in pncconf my io connections are all messed up.  Even though the help output shows the correct pins.   

It looks OK to me

The pncconf pin list can be a bit confusing since it mixes
channel numbers (stepgens,PWMgens, encoders etc)
with GPIO numbers. GPIO numbers are 3 digits

Shouldn't pwm io port 1 show as 1 on the P2 config page? Or does it follow the secondary function numbers?

No, PWM 0 (on P2 DB25 pin 14) just shows up as channel/secondary
function 0 in pncconf. This is also how it's addressed in the hal file,
(by channel not pin)