Ok, I think I understand now. First of all, I'm not sure this will work. Your driver is trying to put out a constant current-what happens when you break the current path (turning the mosfet off)? I would guess the voltage out of the device jumps to maximum in an attempt to maintain the constant current. Then, when the mosfet turns on again, the voltage will drop as the current increases. What is the response time of that current supply? My guess is you don't know, and I sure don't. (BTW, I'm not sure what that bipolar transistor does, but that's just my limited analog skills).
Maybe you can try this: put the mosfet in PARALLEL with the LED chain. (Put a resistor in the path so you limit the maximum current). Thus, you will steer some of the current away from the LEDS and through the mosfet+resistor. As the duty cycle goes up, less average current will flow through the LEDs.