Trying to optimize base period, etc.

Yes, and it doesn't seem to be the reason (unless there's something weird w/ linuxcnc running).

You could try ignoring the warning and then see if anything bad happens.

I found that a CamView tab in Axis ruined my otherwise-good latency, so there are definitely things that can cause problems that don't show up in the test.

Ignore it unless it takes your arm off

Actually I found that my motor-ballscrew ratios were wrong and it gave me 2x leeway. I ran things at 4 usteps and it seems to work. The base time is 100,000. Does that seem reasonable? Steps are 8000 steps/in using a conservative 5k/5k/10k/10k for the step timings. Should be adequate.

nerdsite wrote: base time is 100,000. Does that seem reasonable?

That seems long to me.
There is some advantage in having a shorter base period even if you don't need the step rate, because the step-rate "granularity" is reduced.

I agree, you should run the base thread as fast as you can without getting real time errors.

Running it slower than necessary just increases the likelihood of stalls caused by sub-harmonics
exciting stepper resonances at unfavourable speeds

That's what stepconf creates. Can I manually change this in the ini file?