I just had a helluv a time with my new control system. My servos were locking up but they would not spin with Mach3 active. I found my 5V power source to be the problem. I didn't want to add the extra wire from the computer source so I installed a serparate 5V power supply for the geckos. Well, it didn't work. I also thought I had a parallel port problem with the step and direction signal but it turned out to be the 5V. In my case, the only way to make it work was by tapping the 5V out of the control computer power supply. I'm going to use a game port pin for my final assembly and run a second cable.
Hope this helps. Keep trying, it'll work. The geckos are great controllers and coupled with Mach2 or 3, heck, can't go wrong!
If this doesn't help, post your schematic! There is a bunch of talent here to help out.