Welcome to GotWind!
By "rotor", I assume you mean the propeller rotor? I only ask because you state "the turbine works fine until the rotor is attached", and I assume here you mean that the dynohub works fine until you attach the rotor & blades to it?
Assuming my assumptions are correct (lol), there is no good reason the dynohub would respond differently to a particular type of mechanical input. It should produce X open circuit volts @ Y RPM regardless if it is connected to blades, a bicycle or a hand drill. I will mention that the dynohub is a fairly low output device (1.8W @ 6V).
I am sure Ben will respond, he has built some mini-turbines from dynohubs, and I am sure will provide you some links.
If you post a few pictures, perhaps we can "see" some flaw, but really, it should be pretty straight-forward.