Hi Steve,
I took a look at your configuration and it seems fine to me (although I was missing a couple VIs - my counter group config and my counter source). What I would suggest is switching which analog output connects to which counter. If you notice that the problem follows the counter, then it could be a counter issue. My suspicion however is that it has to do with your analog output not being completely TTL compatible. Therefore, the problem will morelikely follow your analog output. It might be more advantageous to use a digital line instead of an analog output.
Another thought I had has to do with the fact that you will always read the first counter first then you will read the second counter. It could be that the call to read the counter takes
a predictable amount of time the first time but by the time the second counter is read, there is a greater chance that the counter reading is different. What I am trying to say is that the operating system might take control in between when counter 1 was started and when counter 2 was read. This is where variance can be introduced.
Anyway, hope that helps. Have a good day.
Ron
