Hi K80,
Anthony is definitely right. If you're using software timing then you should consider yourself lucky that everything is happening within 1 millisecond and not longer (Windows is a non-Real Time OS, so it can never be dependable to have fast loop rates).
Other things slowing you down are that you're using LabVIEW 6.1 (which only uses Traditional DAQ, which is up to 40x slower for single point operations than DAQmx).
You could do what you are trying to accomplish with some counters and some external circuitry. Essentially it sounds like you are triggering off of an analog level, so that trigger circuitry would need to be external to your device, but you could easily make a triggered pulse off of a digital trigger with a counter and have the accuracy and resolution that you are looking for. I'm not really sure about the details of how to make an analog level trigger, so if you could get some help with that, then we could work on explaining the LabVIEW part. If you could upgrade to LabVIEW 7.0 or higher, then that would also make everybody's life a lot easier once we start trying to think of how to actually do this.
Ultimately though, if you need to do something with <1ms timing, then you will have to use hardware timing or an FPGA.
Regards,