I recently uninstalled my mach 3 program and then reinstalled the program again and now there is no communication between the homemade cnc machine and the mach 3 software. any ideas on how to fix this issue?
That's the "profile" that contains all your settings. It goes in the main Mach3 folder, along with your license file. If you reinstalled from the Mach site, it will have loaded a generic XML file that won't necessarily match the settings required for your machine. If you saved the files from your old installation, you should be able to copy it into there. Otherwise, you'll need to go into config/ports and pins and re-enter the correct information about your machine's pin-out. Once you've done that, save it with a distinctive name, in a safe place...
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