I use both Mach3 and LinuxCNC so if you get stuck again send me a PM. I've had problems with Mach3 for some reason over the past year or so but can't seem to correlate it to a version change. Every now and then it's like the Mach3 pulse driver (can't remember what it is called, but it is used for timing), goes to sleep. When it happens (using the jog keys on the keyboard to move the motors) the motors move very slowly, maybe one pulse every 5 seconds. Rebooting fixes it.
Something else to consider. If you get random extra pulses or missed steps, check your grounding. I've had a hell of time with a high speed spindle because of the electrical noise generated back up thru the motor to the power supply. Using ferrite clamps helped, but what fixed it was either lifting the ground (dangerous) or moving the motor power supply to another outlet on a separate breaker. The way I tested it was to zero the table, holding dial indicators to the x,y,z and spinning the motor up to speed. Prior to separating the grounds I could see x and z axis moving. This depends on the breakout board, drivers, power supply, etc, of course but it was a bear to track down initially. If you haven't, I would ground your table, power supply frame, etc to a cold water pipe.
I use Mach3 on my two stepper driven mills and lathes and linuxCNC on the larger mill with servos. I found linuxCNC's constant velocity path engine to be better than Mach3 and more programmable. Also, if you have any backlash in the system, linuxCNC backlash was far, far better than Mach3, at least the version I use. The problem with Mach3 was that the backlash take-up was done at high speed sometimes stalling the steppers. I disabled it because the .002" backlash I had on those machines wasn't worth worrying about. I since moved to zero backlash nuts on both. Other than that, not much difference.
Jerry