Oh, I should have said, the problem seems to be missing the positive going pulse about one time in 50 or so. Also. this processor is only running at 8mhz.
run1802
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apropos of the polling logic, I realized that given my timing, it wasn't necessary to check for the low condition so I pulled that out completely. I'm now only missing one in 500 or so pulses/characters. The target processor will be 16mhz so the problem may go away completely if the millis update routine completes in <my pulse duration.