It could be the voltage difference with the controller.
It could be the speed sensor(s) on the hub motor send more pulses than a regular motor, and the controller, thinking the wheel is spinning really fast, is limiting the speed. (it would still have full torque on take off, until it reaches said speed though, I would think)
Is the wheel rated for 24 volts or 36? getting less voltage than it's rated for would limit it.
I'm not sure what each wire is for, but you could try disconnecting them one at a time (if they match in color, i wouldn't try mixing them up) and see what it does.