Just a guess -- are you generating a *finite* pulse train on Ctr0? On an M-series device, a finite pulse train requires both counters working together. The one you program explicitly generates the output pulses. The other one is used in a manner similar to a "pause trigger", to precisely control the time period when the output counter is enabled. My guess is you're seeing this single precisely-timed pulse from Ctr1.
With some extra DAQmx programming, it's possible to accomplish a finite pulse train on Ctr0 without having Ctr1's output signal showing up at the terminal block. You would have to configure Ctr0 to use an internal signal "Ctr1InternalOutput" as its pause trigger and you'd have to precisely calculate the correct duration for Ctr1 to pulse (plus get the polarity and idle state right). Then you'd further need to redirect Ctr1's output signal by specifying its "Output Terminal." A special behavior is if you specify an empty string "" for the Output Terminal, then Ctr1's pulse stays inside the board and isn't routed to *any* PFI pin on the terminal block.
(It's also allowed, and much more common, to simply specify that the output goes to a different PFI pin other than the default. Probably something not physically wired anywhere so there won't be side effects.)
-Kevin P
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