5i25 + 7i85S setup questions

Those ini values are _not_ defaults
default servo thread period is 1000000 ns (1 ms) not 100000 ns (100 usec)
default P term is 1000

I've no idea how those values got changed. Odd.

I changed the values to what you said and the square wave on the dir pins changed to an even 45hz on all motors that had previously been active, and some random step signals were going out.

I bumped up my stepscale on each axis to make motor motion more obvious and the problem went away the next time I opened linuxcnc. I'm not sure if it's coincidence though. Thoughts?

I'll keep poking around the configs to see if I can isolate what I did to make the 45hz go away and report back when I do.

45 Hz on direction pins most likely means you had oscillation from bad tuning/servo thread
values (which you did have), Once this was fixed, the problem went away