Roz,
The counters on the PCI-6711 are provided by the DAQ-STC. Unfortunately, these counters don't support a start trigger. Only the NI-TIO, available on NI 660x devices, supports a start trigger. However, the analog output channels support triggering. You may want to consider using the triggering capabilities of the analog output channels. Another option is to gate the counter generating the pulse train. You can use a gate signal to allow generation when it is high (or low) and not allow generation when it is low (or high).
Good luck with your application.
Spencer S.