Why does output voltage increase when pwm input frequency to output enable increase?
Multimeters are not designed to measure anything above 1khz for the most part (look at the specs of your multimeter). The averaging logic built into the multimeter is giving you false results.

Take a look at the signal with an oscilloscope and you should see a 10khz square wave with a pk-pk voltage of 3.3v and a duty cycle of 50%. If not, there must be other issues going on with your circuit.