"Based on what you have told us so far, I am leaning towards the idea that when you are moving simultaneously in Z and X directions, somehow you don't have enough power to not stall the X-axis."
OK i can rule out the z as I have taken the problematic gcode and removed z references. I put and indicator on the machine and taped a pin to be used as an index on the motor timing pulley. I programmed a pause in the code x0.000y0.0000 the readings show a shift to the right 0.003 inches every unloaded (milling air) pass. Absolutely repeatable ten times in a row.
However it could be related to X and Y coordinated motion. I am going to do some further tests this afternoon.
"The x-axis probably takes the most force to move when it is not centered over the saddle. The weight of the table will have more of a tendency to bind slightly against the dovetails and gibs. So, does it matter where the X-axis is when it won't move?"
I think you are referoing to an instance where if i reduced the speed down to below 8% or so the x stoped responding altogether. I mean not even trying to move so i don't think it anything to do with the mechanics. I will test this further.
"What pitch are your screws? Are they acme lead screws or ballscrews? Are you running direct drive? It takes more power to drive regular leadscrews than it does ballscrews.
If you are running direct drive now, one idea might be to change over to a belt reduction system, . A 2:1 (or even a 4:1) reduction would effectively double (or quadruple) the power of your steppers to the screw and because of the speeds at which you are running, might even increase the speeds at which you could run. This would depend on the torque curve of your particular motors."
From memory 10 turns per inch and roughly 3:2 ratio between timing pulleys