USB disconnects

I finished building my Prusa i3 and have it printing. But I am having issues with USB disconnecting my my computer. The only way to reestablish a connection is if I unplug the USB cable and plug it back in. I have tried a different USB cable and different port. I still have the random disconnects. Sometimes it will disconnect after a few minutes, sometimes an hour or more. It happens when I am printing, or not doing anything with the printer. Anyone have any ideas how to correct this issue?

It would help us to know what board your printer came with. "Prusa i3" is a non standard product that comes in many flavors.
-Olaf

I am using RAMPS 1.4 connected to iduino Mega 256 Arduino clone control board. I bought a RepRap RAMPS 1.4 12864 LCD Display 3D Printer Controller with Adapter to print from SD card. But when I print from SD the printer acts erratically. It will print normal then go far to X or Y axis. It doesnt do this when I print from USB (just random disconnections). I have tried 3 different USB cables, different USB ports and different SD cards.