MEGA 2560 - Odd Timer Behavior first loop and intermittent thereafter

[MicroBahner]

@monsterjeepn

When you mention using both OCR3B as well as OCR3A to generate the short pulses,

In this example only OCR3B is used to create the pulse. OCR3A is only used as TOP and should not generate any output. I think you can also use ICR3 as TOP in this case.