Hi Mark,
you need to get a power supply which supplies a reliable current of say 1A at least. Hook up the motor and take care of sufficient spike suppression.
Use 10 to 47nF capacitors from the positive and negative motor terminals to the motor case.
Trying to "read" what's going on at the motor using an oscilloscope will fail since the back EMF of the motor will "spoil" the result.
Reading at the base of the drive transistor (or the timer output pin) you should get a good result reading the duty cycle.
I do not recommend using a bipolar transistor to drive the motor. A MosFet (N-channel) has a typical ON-resistance of a fraction of an Ohm, hence almost no voltage loss.
Even using a BUZ10 (which is overkill to the power of 10) the circuit should work under any conditions. Up to 3A motor current it won't even require a heatsink.
Boncuk