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Looks like HDDs do have interrupts since they are slow and do need the OS to wait for datatransfers.
I'll see if the latency-test will get better or worse when the SSD will arrive

This is what comes up from that link

Alright, understood.
Today I spent some time with my cnc. I setup a new machine in LinuxCNC, and now I have two setups.. one is "good", and the other one shows this issue. 
What I found out - when I startup the "bad" machine and open the "probing" tab, none of the work offsets at the top is selected.
When I start the "good" machine, G54 always is preselected.

No idea if this makes sense or helps, but it fits to the error message imho...

 

Please notice that in step 2 at the end the 4 is missing from amd64
It should be:

$ sudo apt install -t bookworm-backports linux-image-rt-amd64 linux-headers-rt-amd64

Added 2 more.
@tomapc
@toma.cnc1
@toma.3d
@tomaberisha5688
Reminds me, i have to fix the name on the last one as it was the first one i registered.

Looks like 7I77 U15 (74LCX04) receives, buffers, and inverts
the ENCMUX signal to generate the EVEN/ODD signals that
enable the 26LS32 even and odd line receivers, so is a prime
suspect with encoder mux issues: