Carl,
I don't know if anyone has brought this up yet, but how is your system grounded? Early on, my system was losing steps, in part, because of poor grounding. It's important that you have a very solid, single-point ground for everything. This one point should be the ground for the line cord, the motor power supply, and the +5V and +12V power supplies for the CNC4PC board. You should have a single lug securely tied to the electronics case with individual wires running to the various devices from that one point. NEVER daisy-chain grounds from device to device. DO NOT ground the PC to the electronics case. The only connections to the PC should be the parallel cable signal pins, and the USB cable that provides power for the PC-side opto-isolators. The PC ground should not be connected to the electronics box ground.
Also, you should be using shielded cables for any limit switches, e-stops, etc., and those cables should have their shields connected to that solid ground ONLY at the electronics box end, NOT at the switches, etc. Shielded cables for the steppers also would not hurt, as long as you connect the shields as above.
What rev of the CNC4PC board do you have? If it's an early one, you really should get an updated one, as there have been a LOT of design improvements made. My rev 2.0 board was very unreliable in my system. It drove me crazy for weeks! The rev 7.0 board I now have has been bullet-proof.
If you want to bypass the CNC4PC board entirely, wire the PC parallel port connections directly to the Geckos (they're internally opto-isolated), and wire the +5V from the USB cable to the "common" terminal of the Geckos. That's all you need.
Regards,
Ray L.