Chris,
I would try a more methodical approach than just "running some Gcode". Make a single axis program, consisting of very short, medium and very long movements. Check the distance moved after each single command is read.
Check the distance moved in jog mode. Does it correspond to the display? Again, try short, medium and long movements.
Check how accurate the machine returns to position after running a simple positioning loop: forward and back to the same two endpoints. Do it once, then several times, to see if you can find a systematic error. This is how you troubleshoot, not by running actual programs.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)