One possibility would be the crystal frequency used for timing.
You are heading down a blind alley on this one. Ray Gralack has been doing some development with APCC that may answer your issue.
If you really want to check your RA driving rate you can set the rate to Stop, place a piece of tape across the stationary and moving part of the RA axis. Cut the tape at the seam between the axis. Get an accurate timer, set it to the sidereal day (23hrs,56min, 4.09sec). Push the timer and set the rate to Sidereal at the same instance and let the axis track until the next day. Check when the tape lines up exactly with the timer. Or you can set it to Solar rate and set the timer to 24 hrs. We have done this a number of times with mounts that people swear are running fast or slow and every time the results are within a small fraction of a second.
From: Craig Young <craig.young.m8@...>
Sent: Tue, May 5, 2020 4:23 pm
Subject: [ap-gto] Adjust CP4 Clock Frequency
Rolando mentioned in a recent posting (#70144) the tracking rate is dependent on the controller clock frequency. Over the years of using my AP1600 with encoders I could never get APCC to provide the same tracking accuracy as other users, even with a 200 point model, so it had to be a problem with this particular mount. Since this has never be resolved after several hours working with AP I wrote my own tracking program ATRACK which does provide very accurate tracking over several hours.
With ATRACK I know exactly what the RA and DEC tracking rates are because the target drifts no more than 1 or 2 pixels over 4 hours, without the use of an autoguider. So comparing the 200 point model tracking rate with ATRACK I noticed a consistent error, in both direction and magnitude, which led me to the conclusion there is some base tracking error in the mount that APCC does not correct for. One possibility would be the crystal frequency used for timing. This is a known problem in radios which is why they revert to TCXO devices (Temperature Compensated Crystal Oscillators). Also, on one of my other mounts, there is a setting to adjust the master clock frequency. I know the basic tracking of the mount is excellent because ATRACK reports no sudden jumps (e.g., cable twists or mirror shift, etc). And, if there is a clock frequency error then the encoders will provide excellent pointing (which they do) but accurate tracking would not work. A 200 sample pointing model can provide excellent pointing and tracking but the tracking makes an assumption the sidereal tracking rate of the mount is perfect. If the sidereal rate is too fast, like on my mount, then the model will not know this and accurate tracking is impossible no matter how big my model sample count or polar alignment.
To test this I ask the guys at Astro-Physics if there is a way to adjust the base clock frequency of the CP4 using APCC. I made some quick measurements comparing ATRACK rates with APCC rates and found a discrepancy of 0.1% (0.001). Since APCC is ALWAYS running fast I would then reduce the clock rate by 0.1% and see if it solves the problem. The adjustment should reduce the tracking rate to match ATRACK.