I'm surprised the motor turns at all, and I'm also surprised you haven't burned out the USB chip.
The Arduino power supply is not designed for high current devices (like motors). The 3.3V supply is from the FTDI USB adapter IC and is only capable of supplying a few tens of mV IIRC. The 5V supply is typically from USB, where you have at most 500mV total.
I suspect the behavior you are seeing is because the excessive current draw of the motor is causing the ATmega and/or the FTDI to brown out and lock up.
You need a separate power supply for high current loads. Check out this tutorial
for more info.