RPM measurement using quadrature encoder
Ensure the encoder outputs 400 pulses on each phase. It could be 200 on each phase for one rotation

Rather then clearing your pulseCount, figure out the time it take to make one rotation (as close as you can tell) and turn the motor on for only that amount of time, and then off again. This will allow you a more controlled environment to test your code in, and it will be the same(almost) every time. 

You are calculating revolutions per second with your code, not per min 
number of pulses/400(if this is correct number)=Revolutions     which you are clearing ever 1000ms

Ensure good connections on your wiring as it does not take much to allow the interrupt to fire twice when it should have only fired once. 

Use the second phase of the encoder, this is what gives the ability to decipher bad signals and change of dirrection,   ie- multiple A pulses in a row(without any B pulse) does not equal movement, it means either the motor is hanging out right on a phase line, or something is causing the interrupt to fire more often then it should.