Problem with Mesa 7i96s and spindle control

Thank you for responding. I am sorry I did not include more info. My board is a 7i96s and now I have encoder feedback. Turns out there was a wiring error. Now I have negative values and way off when doing M3 command. I set my amt102-v to 1024ppr so i was using 4096 in pncconf. I am new to this so using pncconf appeals to me for as much of the build as I can.
I am curious if the mesa config is better than the pncconf and can I make a separate profile in it? I was working on getting the encoder working and at the same time I changed some settings and now my spindle does not work. I have the m3 come on and the vfd shows hz rising and then stabalizing but the fan on the vfd does not come on and i have no 3 phase coming out. I should not have been messing with the wiring and at the same time changing settings and will try not to do that again, but for now I dont know which one it is, the settings in pncconf or a wiring issue.

I changed your Topic title to something more descriptive.

You might want to give some more information on your vfd and how you have wired it to your 7i96s.

One way to help diagnose this (assuming it's a hal issue)  is to run
LinuxCNC, and then turn on the spindle at 1/2 speed.

Then, in a terminal window, type:

halcmd show all | grep spin > spindle.txt

and post the created spindle.txt file here.