The USB controller will only work with the Planet-CNC software. This software is well made and will provide great functionality. The planet-cnc software delivers instructions to the microcontroller on the board and the microcontroller will send out the pulse trains needed to move the machine correctly.
There are two main alternatives if you want to use the mach3 software:
First, get a parallel port card and add it to your computer and get a parallel breakout board. If you have a laptop/notebook computer, this will not be possible.
Second, if you have a laptop, or really want to use the USB as the main interface for controlling the machine, you will need to get the smoothstepper board which works with mach3. The price combination is much higher than the USB controller with planet-cnc, but will work with Mach3.
The planet cnc controller can be prone to electrical interference and has been known to cause such problems. In the first instance try to use a quality double sheilded USB cable, hopefully this will fix your problem. Alternatively you may need to sheild your limit switch, estop and or motor cabling. My pick is that a quality USB cable will fix it though, worked for me.
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I have your USB controller sitting here and want to control it with something other than PlanetCNC control software?