DuaneB:
Not sure that that is what anyone was suggesting - for a time critical application most of us would just set up the hardware timers to do their thing in the background. They are entirely hardware based and not effected by whatever the software is doing elsewhere on the micro controller - until you want to effect them that is.Look up the hardware timers in the datasheet, its not the easiest reading, but there are various waveform generation modes built in to do exactly what you want without software or interrupts getting in the way.
Duane B
Hi,
I didn't look into it completely but the Timer0 that arduino uses to generate the millis() was the problem and since my app is time sensitive I couldn't have it pausing my real program or interrupts (timer0 is a higher priority I guess?) every 1.024mS with a 5uS freeze.
Either way about it, disabling that Timer0's interrupt means the only interrupts that run are my own which is exactly what I happened to need.
Thanks again for the help guys.