I was testing last night, and had no problems at all! I couldn't figure out what was different, but then I realized I was using the battery. All the problems were happening when I was using external power plugged into the wall. I'm not sure why tha would cause a problem.
Perhaps a difference in grounding?
OMG ... can't believe I just let these posts fly by and miss the obvious!
Are you using batteries or a power supply for the camera? Or as part of the USB remote circuit? I have assumed you are trying to get "precision sync'd" shots while also doing PTP communications? If so, there is no need for any external power on the USB connection. A standard USB cable with a switch in the +5V line is all that is needed.
If it's a camera power supply then reyalp's comments about grounding are appropriate.
If this does not make sense, a wiring diagram and/or photo of your setup would help here!