Powering up arduino with Xbee and a 6V (run on 5V) motor
I have a lot of bad experiences with motor noise, and I am not an expert on this subject but I guess your problem is from the noise caused by the motor (both electrical and electromagnetic noise). Just google DC motor noise and you will find tones of problems and answers on this topic.

What I would do is to try to isolate the power of the DC motor (the driver) as much as possible from the power of the Arduino (they say that in some cases, using two separate PSU's should be best, though I think not too practical). Also, you didn't mention motor specs, but be adviced that the capability of the 5V supply of the Arduino is very limited. So try double check how much current the motor draws (especially when it stalls), and how much the 5V line of the duino can supply. I don't think the 5V line is up for the job.

I would never supply a motor with the 5V of the Arduino.
Also try to keep the motor physically far away from the Arduino.

When there is noise caused by the motor, all kind of funny things will happen, and unfortunately it's not very easy to tackle.

I hope some more knowledgeable ppl will provide you will more detailed advice.
Dave