Just to make sure the acceleration wasn't a problem at all, we dropped the acceleration down to 3 in/s^2. Halscope screenshot is attached -- no real change. The initial lag is still around 0.002-0.003 inches.
It exactly matches the acceleration time period, and then jumps into position almost vertically. It's almost like something is holding the motors back during acceleration.
You might try increasing the drives velocity loop gain (increase till it oscillates then back off 20% or so)
while linuxCNCs P term is low to see if that helps the lag.
the fact that its unaffected by acceleration does suggest mechanical issues though
Just tried increasing "speed loop gain adjustment volume." It did help a teeny bit. We increased it 2 'gradations.' On the 3rd gradation, it started buzzing as soon as the drive was enabled, so we backed it back down to 2 gradations.