If this issue is random that leads me to believe there is something going wrong with the hand controller or gemini controller. I've been troubleshooting some odd PEC issues lately on a new G11T and along the way I reflashed everything which only caused more random issues. It wasn't until I RESET the SRAM that things went back to normal. In addition I believe I've solved my PEC issues by leaving the hand controller disconnected altogether. I'm just imaging so I can do everything I need to from the web interface and ascom driver.
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The issues I was having with PEC is that it would drift after a few hours... so I'd run pempro, generate a curve, upload it to mount and then have fantastic results for a bit. Later in the night or the next night PEC would start causing more problems then it solved. Leaving the hand controller disconnected seems to have fixed it for the last four nights. All operations and guiding have been fantastic. It merits further investigation.