I also charge my nexus from a homemade dock at the 1000-1300 mark compared with my usb port. The usb port is so bad that most of the time I see it discharging while in use!!!
I believe this is a hardware fault as mine used to charge great through usb. at one point my usb socket stopped working altogether, I ran a soldering iron over it and it is at least working again, still slow to charge.
I have also been following a thread about this in the google user forums. One person stated that when they changed the usb board charging rates resumed to normal standards. There is a lot of people in that thread suffering from this. Bad show google.