I too have seen that PemPro curve results discrepancy on runs east vs. west side of the mount.
I REALLY like your explanation, on the cause – even if the results might sometimes be slight. They could be further exaggerating with poor seeing, besides the atmospheric component adding to the discrepancy.
Yes - if you run PemPro with the “standard” setting of 5 minutes (deg ?) looking toward the east of PM, the OTA is “rising” and the atmospheric refraction is “actually improving”, all during the hour long RAW data sampling.
On the flip side, running with exactly the same PemPro meridian target offset, the atmospheric refraction can ONLY “degrade” steadily for the entire western sky target run.
So, you have the worst of both situations. You can either trust the optimum raw data when PemPro runs from the west side of the pier on eastern targets, or the twice as bad situation with “STEADILY declining” target Altitude ... when running with the scope on the east side (looking west).
I brought this up, on this Group probably more than a couple of years ago, suggesting that PemPro could be run twice, and the two raw data curves averaged – or their samples interleaved – to come to some averaged curve result. Requires some further thinking, whether the results “should be weighted” more toward eastern targets, Something for Ray to consider, based on your premise.
Anyway, Rolando, thanks for this explanation of what has been frustrating me about my own PemPro results ... for a VERY long time. Unfortunately, in the short term, we just have to live with this minor discrepancy.