Hello, I was also having this problem with my series 1 machine.
What fixed it for me was changing the computer BIOS USB setting to "Full Speed (12Mbps)' instead of "Hi Speed (480Mbps)". Lowering the transfer rate is a common way to help with long cables.
My shuttle is plugged into port on the keyboard. Then the keyboard needs a extension USB cable to reach the computer. Not that I've measured the total length but I'm guessing it's over 10'.
Tormach PCNC1100, Mach 3 R3.043.037, MastercamX5 level 3.