I am not sure if the PID settings in Mach will do anything at all, I would imagine it is all in the plugin.
Below is a screenshot of my spindle page, afraid I don't have a pic of the PID settings though.

What I actually did was used the autotune to get the spindle close and then tweaked from there.
As the spindle does not have an autotune I just set it up as an axis and then once done disabled the axis and entered the settings manually in the spindle page.

Not sure if that is possible with yours or not as I am not sure if yours is a servo or not.
Hood

Did you move the encoder wires over to the CSMIO/IP or were you able to select the ENC encoder channel? It would be easy to just move the ENC terminal block if they had made the pinouts the same..

I use the motors encoder for feedback.
It is a sine/cosine encoder  it goes to the servo drive I then take the Servo Drives encoder outputs and ,if I recall correctly,  feed them to the IP-A and then just jumper them across to the Enc module.

Hood

ah ok.. I may try that to auto-tune and get the PID close.  Thanks

Do you not have it that way already?
I know you have Closed Loop disabled but did you not have it enabled before?
Think if you have closed loop chosen you will need feedback to the IP-A, could be wrong though.
Hood

Yes I had tried this as closed loop throughout this. I was seeing weird things with M3 M4 not working and kept trying many settings. It seems that certain settings like Spindle Pulley don't take effect until you restart Mach3 but I can't be sure. There were times I restart Mach3 and the motor control would act different. It has always bothered me that the Plugin Spindle Axis config screen has the "Encoder Input Channel" I used when the encoder was connected to the CSMIO/IP-A.  I assumed once I got the CSMIO-ENC and moved the encoder to it's Channel 1 input, that setting would have an option for the ENC channel, but it doesn't.  I had considered doing what you mentioned and jumpering the two encoder inputs of the IP-A and ENC in parallel but was concerned about creating signal problems.

This is my spindle encoder

That encoder should work fine.
Hood

I could not get the CSMIO-ENC option to "Align at stop" to work. I moved the spindle encoder to an axis encoder input, configured it as an Axis and it did autotuning the PID. It worked fine.  I put those settings in the PID settings for the CSMIO plugin/spindle section and the spindle just revs up to very high speeds when it should be 0 RPM.  I am sure the encoder is fine and wired correct because the ENC plugin monitor shows correct angle movements and correct RPMs.

Asked CS-Labs how to tune the PID on monday and still no response.  My ENC firmware version = 1.02  I was curious how that gets updated? When you update the CSMIO/IP? I see no separate firmware downloads for ENC on CS website.  I ended up using a macro to read the ENC angle value to orient it manually.  

Youtube of ATC dry run with spindle orienting. Have to slow way down to catch angle data from CSMIO-ENC -- GetInput(84).  
https://www.youtube.com/watch?v=TZEntieCl_Q

Youtube of the tool change, sorry the air compressor is so loud..
https://www.youtube.com/watch?v=9PaKyMAdqDM

Thanks for all the help, Hood

So you are saying the spindle runs away at full speed with the values you had for when an axis?

Did you set the pulses per rev accordingly?
Do you have the encoder direction set the right way, ie does it help if you choose the Inverse option?

I think the modules get updated from the firmware you download for the main controller, been a while since I have seen them update but occasionally they will when I load new firmware.

Looks to be working good
Hood

Yes, it runs away.. pulses set correct.. encoder direction based on + RPM properly displayed.. 

I got a very detailed email on this from CS-Labs this morning.  Quite a bit of effort to outline the settings/issues that hopefully they put on their website.

Couple big items were:

1. They said the encoder from the motor itself needs to go to CSMIO/IP-A, the encoder off the pulley 1:1, goes to the CSMIO-ENC.  This won't work for me because the actual motor encoder is connected to the Siemens 611 drive controller.  I don't want to take it off that.

2. They said "Align at Stop" is not for tool magazines. It is intended for lathes.

I will leave it as it is with the Macro orienting the spindle for tool change.  They gave me another macro technique using plug in calls I may try.  NotifyPlugins() which I hadn't used or known about.