The Hardware PWM is like the Energizer Bunny.
It keeps going and going and ....
And in the middle of the main loop, his going problem is getting really bad.

Got to be something in there to disconnect the furry little b_______.

A timer could work, a software loop could work. something to stop it after 1ms (maybe a PAUSE 1).

Depends on what you want to shoot the Rabbit with.