Disable the MacBook's IR Receiver (System Preferences, Security, General) and see if that makes a difference for you.
USB port inequality is a known-issue with some MacBooks. The reason is that the internal USB devices (camera, IR receiver, keyboard, touchpad) are on a hub with one of the ports, creating a potential overload. The configuration varies from model to model.
Here are a couple articles; one old, one recent:
http://www.wired.com/gadgetlab/2008/05/the-macbook-all/
http://www.djtechtools.com/2010/07/1...rt-inequality/
I'm on a 13" MacBook Late 2008/Aluminum (not a MacBook Pro), with Snow Leopard (10.6.5). My 950 and 350 connect and charge seamlessly on either USB port. I even turned my IR receiver back on and the 950 still connected, but it might make a difference for you.