Very strange behavior

I was the one having trouble with the parallel port, I solved that with a PCIe port add. Now I get movement on CNC with using directional keys as long as speed is below 30" a minute for jog, if faster I get like stuck sounds and no movement. I attempted to run the test file above the board without the bit itself running, it lifts the z axis and stops, on the computer screen it appears to be moving but seems like it lost power to motion controllers, the lights on all 3 go out. I did have to invert the z axis, it was going up when its supposed to be going down. 

I'm sure it's a settings issue, I have a Sain Smart 5 axis (Only using 3) that has parallel port for com buy uses a USB for power only. I was using the very old linuxCNC that would pop up no longer supported and worked fine, trying to change to this is giving me a headache so far....

Just to let everyone know, I have LinuxCNC 2.8.1 I thought I might need 2.7.14 and installed it but got no response from the CNC at all, was like it wasn't connecting at all to the Sain Smart board.

Try powering the breakout board from a power block instead of from the PC.

tried that and didn't make any difference

I think I've figured out I need to slow the communications down between the computer and CNC, I'm not sure what settings do that though.

On a parallel port machine there isn't really "communications" between the PC and the machine. The PC is just sending step pulses. And there are limits to both how fast your PC can generate those pulses reliably and how fast the stepper driver can receive them. Normally with a parallel port config the limiting factor is the maximum speed the PC can generate them. The best way to do this is by choosing a maximum velocity that falls within your PCs capability. You calculate this from the step scale you are using. If the maximum step-rate is unacceptably low, re-examine your micro-step settings in your drive and choose a lower micro-step setting. The micro-step setting generally has little bearing on the machine's true resolution since micro-step accuracy beyond about 4x is mostly meaningless except for improving resonance harmonics.