I'm guessing that whenever this is executed:
Code:
HPWM 1,DutyCycle,10800
PBP is stopping, setting up and restarting the HPWM.

If you do this in the loop,
Code:
CCPR1L = DutyCycle
then your problem should go away. I don't know if PBP allows you to do this. If not, you will have to set up the hardware manually.
Code:
PR2 = 462  '10,800Hz frequency
CCPR1L = 0  'Initial duty cycle
CCP1CON = %1100  'PWM mode
T2CON.2 = 1  'Start TIMER2