To a mac?
Don't shoot Nikon but Canon and I've had on and off problems with long usb extensions. I've had zero problems with a windows machine but so so luck with Mac.
I'm working now, on 10.8.2 with the only extender I have used at works, a Sewell.http://sewelldirect.com/USB-20-Active-Extension-Cable-34-ft.asp
Works great until it gets dropped a few too many times then it does exactly what you are complaining about. The cable will still work great with a windows machine.
Put a new cable on the Mac and it works again, at least until the cable gets flakey.
Next time I order I'm going fro dual 15' extenders instead of a a 32'.
BTW, you can due usb over cat 5 but be aware that the reasonably priced ones are USB 1.1 and they are painfully slow to transfer files. 30 to 45 seconds for a single file to make it to the computer from a 5dII
Usb 2 cat 5 is a WHOLE lot of money.
BTW I have the same issues regardless of program, C1, DSLR Remote or EOS Utility