mesa/gecko setup losing steps only at very low pulse rate

I have been messing with this for a while but previously didn't realize what I was seeing because I mostly use my mill as a router, cutting long straight lines.  A while back, I blew up my previous Gecko drivers because of a wiring fault in the house that resulted in 110V difference between the stepper motor drivers and the linuxcnc machine, so in replacement I got a new computer, with a Mesa 5i25, and a Gecko G540 setup.  I'm running linux 2.7.14 with a Sherline milling machine.
What I'm seeing is that on fast single axis feedrates, like 1-75IPM, the motion control system works perfectly.  I can set it up to move from (G20) X0 to X1 and back a hundred times with no accumulated error.  But if I set it with feedrates below about 1IPM (more specifically at about 0.65IPM) it doesn't drive smoothly.  The stepper will move several steps and then miss a few steps.
This is a disaster if you're trying to cut circles, because one axis inherently has low feedrates at the point where the other axis is at full speed.

Has anyone else seen this?  I've done some searching here and in other places and haven't found anything.

I ran into this previously when I was trying to set up a fourth rotary axis, and it was seriously misbehaving because its feedrate is extremely low at large diameters for keeping the SFPM reasonable.  I thought I was just setting up the rotary axis wrong or maybe the stepper motor wasn't working right.  But now that I'm accurately measuring on a linear axis with a dial indicator, I can clearly see it misbehaving even on linear axis moves.
 
This was not something I noticed when I was using a parallel port, driving the Gecko 203's I used previously.  I think I was using an earlier version of LinuxCNC, though.

Any suggestions welcome.
 

This appears to have worked. Thank you!