MEGA 2560 - Odd Timer Behavior first loop and intermittent thereafter

[monsterjeepn]

@DrDiettrich

Right, but the counter continues counting until it reaches its TOP.

In timer mode 4 (CTC), TOP is defined by OCR. Also from the datasheet, section 17.9.2, page 145:

In CTC mode the counter is cleared to zero when the counter value (TCNTn) matches either the OCRnA [mode 4] or ICRn [mode 12].

However, I'll grant you that I may need to shift to mode 12 in order to have both outputs generating the same waveform, since the datasheet specifically states "OCRnA", rather than "OCRnx". However, it will still be a CTC mode, and the TOP value (half period) can still be defined and adjusted during runtime.