Hm, could be the USB D- signal not getting through (pin 2 of the
mini-B connector.) I would at least resolder pins 2 & 3 of the connector (D- and D+, top-left and bottom-middle in your picture above) and check if the traces are still connected to the pads (mechanical movement of the connector can break the pads of the traces. Hard to see in a picture sometimes.) May as well resolder the pads on the controller socket these lead to (5th and 6th pad from the left in the connectors top row, same pic.) Check the corresponding pads on controller PCB as well. Also, take a closer look at the joints of the following components on the controller PCB: R113, R114, R106, R107. Resolder if something looks bad.
If this doesn't fix it it's very likely that the controller is toast -- can happen if there is some form of voltage spike (lightning, static discharge), although that's very rare and I would expect other problems w/ the computer the board was connected to after something like that. If you have access to a known good RK-9000 you could swap in your controller to see if it's ok.