With Counter Control VI, and NI-DAQ 6.9, there is a "wait" control code. If you first configure the counter for pulse train generation, and then use the Counter Control VI with the "wait" control code, when the code reaches the Counter Control VI, the thread that the VI is in will sleep until the rising (or falling) edge of the counter.
You could modify the Generate Pulse Train (DAQ-STC) VI in ~\labview\examples\daq\counter\daq-stc.llb to do this.
Chad Humberstone
Applications Engineering
National Instruments
http://www.ni.com/ask