Have only had time to skim through the thread. A few additional comments:
1. Your experience of needing to request a period of 73 "ticks" in order to get an actual period of 57 ticks is definitely not normal. I'd be *very* reluctant to depend on any solution that continues to depend on such an odd discrepancy.
2. Just looking by eye, the incoming pulses look a little cleaner on their falling edges than their rising edges. I would recommend an additional configuration step that would make your pulses depend on the falling edges rather than the rising edges. It should at least be helpful for troubleshooting, and is probably a good idea in the long run too.
You'll need to use one of the DAQmx property nodes. I'm not at an LV box to check now, but I think you might find it in a DAQmx Channel property node. I'd look in the region of Counter Output-->General Properties-->Timebase-->Active Edge, or somewhere roughly sorta around there. There's a property in there somewhere where you can specify whether to react to rising or falling edges of the signal that is acting as the timebase, in this case an external signal wired to a PFI.
3. The latching behavior is also not normal. I don't have any real good ideas. Are you checking your task's error out cluster for any clues?
-Kevin P.
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