AWOL:
You're bound to get glitches (they're not random, BTW) when the timer overflow interrupt occurs.
Why not use the timers to generate your waveform, and reserve the processor for slower stuff?
I would love to do as you've described, however you're implying using interrupts and this 5uS 'pause' exists anytime interrupts are enabled and it messes up my signal.
Can you explain or point me in the direction of what is causing this...I've run out of ideas for tracking it down? You mentioned a timer overflow, I wasn't using a timer in my code, perhaps you're talking about one Arduino uses...do you know where that is in the Arduino C files so I could modify it to get rid of this?
Thanks again.