Hi Chris
I'm pretty sure PE cycles through every 8 minutes. Looking at your first graph your run appears to roughly finish around the 5 min mark? That would rule out PE as your major problem because you wouldn't see the RA graph rise and fall that many times in 5 mins due to PE.
I suspect seeing is your major problem, as it is for us all.
Try a higher exposure time of 2.5 to 3 sec and increase the RA min move so you're not sending guide commands every exposure. This may help settle the RA down a bit.