Hello Brian,
Welcome to the forums and thank you for including the code which work correctly with no modifications.
I think your connections can be causing this issue since your counter should be able to do this. I have run your program and externally connect the output signals to the AIs of your DAQ card. I have included some screenshoots to show the results not only with the values you mention but 5 times more than that.
I have also seen the signal correctly on an external scope. Perhaps you could include some screenshoots of your measurements to better describe the issue and possible cause.
To simplify your code, you might want to use the finite pulse generation (not sure if this is an option for your application).
Hope this information helps.
Gerardo O.
RF SW Engineering R&D
National Instruments