Similar situation a few years back with my D700 on top of tower to shoot a ceiling fresco.
In my situation, I was beyond the maximum length of USB cabling by about two meters. I'd get a half dozen shots and Nikon Contol would beach ball and I'd have to force quit, loosing the last image. From what I understand, it's the timing that's the issue, not the length of the cable. It worked well enough for me that I didn't have to get repeaters, though any longer I would have needed them.
When running Control to your Mac/pc, I don't think the images are stored on the camera and are simply downloaded to a folder on the host computer.
That said, the issue sounds like a cable issue, either longer than 3 meters or running a marginal quality cabel or extension cable.