Though I've actually got one of those fans, it's in a box in my storage building... it was given to me. I think they have to be wired into your HVAC system to turn on when the system turns on. So you'll probably need an HVAC guy to come to set it up. But it should work if its just a long run and not enough force to get it there.

Or... you could have an HVAC guy come out and balance your system. It should have been done when originally set up... but rarely is on residentual setups. They check the flow of air through the system and make sure it's all getting the same amount by using baffles.

Have you checked to make sure that all your lines are connected well and not kinked? Mya be something simple. Insulation in the vent?