I was using a 14:1 geared extruder with 1/32 microstepping (DVR2588 driver), and I noticed that the printer was not reaching full speed. I kept trying to speed it up with M220 to see if the smoother drive would help prevent skipping, but it never got faster.
The extruder step rate seems to have been the problem. I just switched the machine to a direct-drive 1.75mm extruder, decreasing the motor steps to extrude the same volume by a factor of about 4.5, and the machine prints a LOT faster… except when minimum layer time comes into play, which now is almost always.
I can haz Cortex M-series?