I can't advice you with your current problem as I don't know the mach3 software that well.
But a number of months back I upgraded my main CNC computer with some newer 2nd hand parts, and I had nothing but problems, stalling, missing steps etc.
I tried meny version of Mach3, I tried Windows XP, and Windows 7, and still the same problem.
I gave up in the end and put the old parts back in, and it has worked fine since.
The newer mohterboard was an nvidia nForce 4 chipset, and the old motherboard was an intel chipset.
You do say that your computer is using the nvidia chipset, So I don't know if mach3 don't like nvidia chipsets.
What make and model motherboard is it you are using, my problem motherboard was a FoxConn NF4SLI7AA-8KRS2.
Best Regards.