How to fix "Queue is not empty after probing"

what are you using the base-thread for?
10000 seems incredibly small.

if you are using custom kinematics, you might have to build again from source, you may not be able to use my debian packages.

It requires you to be logged into github to get the debs I think.

The default setting of 20,000 corresponds to a maximum pulse frequency of 50 kHz. An LPT system with a high-quality cable and control board can handle much higher frequencies. 10,000 corresponds to only 100 kHz. I managed to stabilize the latency test at a level no higher than 2500.
My stepper motors run at speeds of up to 20,000 mm/min.

Ok, I'm not sure I can help you with the latency and the Y errors way out of scope of the probing issue, you had another 2.9 that was working ok, where you could patch my changes?