yuany,
I'm not at a computer where I can open your vi's, but I'm pretty sure I know why you're having a problem. When you create a FINITE pulse train, DAQmx automatically sets up the additional "paired" counter it needs for the task.
The counter you specify creates a pulse train that is output only while the paired counter is generating a single hw-timed pulse. The combination of the 2 generates an exact # of pulses.
Ctr0 and Ctr1 are paired, so you can't output a finite pulse train with both at the same time. If you were to use Ctr0 and Ctr2, you'd be ok. (Note that DAQmx would automatically program Ctr1 & Ctr3 to support those finite pulsetrains.)
Final tip: since you want to specify initial delay for the counters, I think you'll probably also want to configure both to be started by the same digital start trigger. That'll preserve the timing relationship between the 2 outputs. It's possible to specify a digital bit as the start trigger which you can then fire programmatically.
-Kevin P.
CAUTION! New LabVIEW adopters -- it's too late for me, but you *can* save yourself. The new subscription policy for LabVIEW puts NI's hand in your wallet for the rest of your working life. Are you sure you're *that* dedicated to LabVIEW? (Summary of my reasons in this post, part of a voluminous thread of mostly complaints starting here).