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Guys are you arguing about two different things here ?
Autoguiding with a PEC enabled mount ?
Autoguiding while trying to collect the initial PEC data ?
Quite different questions with quite different answers, that may vary with the gear and software in use.
The PEC data collection process needs to be within one loop, so you cant have extraneous corrections going on that the PEC program doesnt understand is happening or at least is managing itself in some way.
Once you have PEC enabled then you have (hopefully !) corrected much of the mounts periodic errors and autoguiding is now only trying to keep up with all the 'other' problems but not periodic error.
During PEC data acquisition the software frequently uses the guider port to make the corrections, but it knows its making these corrections and adjusts the data it records for those corrections.
But different systems do things in different ways.
I have no experience with the CGEM process, so I cannot speak for that one.
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