I'm not sure of the exact workings, but Mach will certainly read the entire file when you load it to check for errors and generate the tool path, however I doubt the file will be cached anywhere, as the memory requirements for large files would be too high (probably not by modern PC standards, but certainly for PC standards when Mach3 was originally written!)

I suspect after the initial run through of the file, the trajectory planner will then re-read the file as required to create the necessary motion buffer. It'll be the continual opening/reading/closing of the file that could cause issues, if the USB device was to enter low power mode.

If this is your issue, it should be easy to test. Simply copy the files to your hard disk, and try running them from there. If everything starts working smoothly with no glitches, then you've most likely found the problem.