I think I've celebrated too soon. Exporting a pulse train from the 'Generate Pulse' vi must not be derived from the camera's clock but the image grabber's clock, this does me no good.
In comparing the output of the Horizontal Synchronization signal and a counter where the source of ticks is a 1MHz pulse from 'Generate Pulse.vi' they gradually walk out of sync and after several thousand lines, are off by one line. Since the camera's buffers are being triggered this is not a scrolling effect but results in a jitter of 1 acquire line from the camera.
Am I naive in trying to synchronize a camera to a DAQ with the precision of 50us (period of acquiring one line)? Other people must need this type of precision. From here I think the only option is to use the 'Horzontal Synchronization Pulse' to trigger a retriggerable counter that puts out the number of pulse I need where each pulse is shaved to be retriggerable by the next 'Horizontal Synchronization Pulse'. This is less than ideal but are there any alternatives?
The pulse train is generated by the image grabber's clock but it can be exported on both RTSI and CC0 lines, which allows you to sychronize both your camera and your DAQ with the image grabber. If you only output on RTSI then your camera will not be synchronized.