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PHD2 doesn’t interact with NINA in this way at all and it has no awareness of focuser or filter operations. The overall architecture is that apps like NINA manage the imaging session and tell PHD2 what to do. The dither and settling parameters are part of the NINA options and that’s where you specify things like settling time. For something like focusing, the usual approach is for the imaging app to either pause or stop guiding, then resume after the focusing operations are complete.
Bruce
In particular, look at the 5 arc-sec tracking error that occurred during a 30-sec period as shown by the arrow. You haven't said anything about your overall setup - for example, can we assume you're using an OAG on the main scope? What gear is riding on the mount? Can you be certain that nothing in the payload on the mount is moving around to produce this kind of error? Were you operating in windy conditions?
Looking at your longer guiding sessions, it looks to me like you had poor seeing conditions. Remember that the Dec drive is idle except for the very short, small guide commands. Here's a look at a typical sequence of Dec behavior:
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