I think I have a defective NXT brick. It has been programmed to move in a direction for 1 second, wait 1 second and then move in the reverse direction for 1 second. The code downloads on another brick and works fine. I have tried changing the battery pack, changing the motor, changing laptops, changing usb cords, cables, etc. and bricks. The problem has been isolated to the brick. I tried a soft reset and ultimately a hard reset with new firmware download and nothing works. I am truly perplexed. I am using Windows 7 and also tried it on XP. The motor will run in one direction. It starts off slow, speeds up, pauses, and then goes faster. When I turn the brick on, the motor runs briefly before the NXT chirp sound comes up. Yes it is plugged into the correct motor port.
Looks like it might be a defective motor driver chip (though they are pretty tough!). What happens if you connect the motor on another port of the same brick? (with program change to reflect port modification)