I have contacted Ultimaker via the support ticket page but haven't heard back. I also pointed them to this forum thread. I rechecked everything and confirmed that the problem is definitely with the x-axis output. The motor, drive train and polulu driver have no effect on the problem. This is what I get when I reset the Arduino:
With Marlin Firmware
[19] Initializing Serial.[19] Attempting to reset RepRap/Ultimaker (pulsing RTS)[19] Unknown: marlin u0.9.3.1[19] Unknown: sd init fail[19] Ready.
With Advised 5D Firmware
[20] Initializing Serial.[20] Attempting to reset RepRap/Ultimaker (pulsing RTS)[20] Ready.
The problem is similar with each firmware except that I get a few more moves out of the 5D firmware before the motor stops responding.
I now note that when I first power up and connect the machine I can issue one to three commands via the x-axis driver and the machine responds. After these initial commands, the motor stops responding. If I then power off the board with the switch, but not unplug the USB cable and power the board back on, the motor will again respond to one to three commands. The whole time the Arduino is connected via the USB cable and ReplicatorG stays connected.
I have another Arduino Mega on the way, I figure you can never have too many of those. If that doesn't fix the problem, then it would seem that it is in the Ultimaker board somewhere. This would be supported by the fact that power cycling that board allows me to issue a few commands again. I'll try to contact them about what it would take to get a replacement board.
In the meantime, I want to thank everyone for the helpful advice and if anyone has any other ideas I'm all ears. A little frustrating to be so close and yet so far away.