Tom, I have a couple of suggestions for you:
1. Your program does not follows a real sequence, that is, there is no way to tell whether the triggered acquisition was set up before the DAQ trigger or viceversa. You might want to put your program in a logic sequence to force the program to execute in the proper order. Use the error cluster to wire all the VIs together and not in different pieces.
2. I see that one DAQ portion references to RTSI2, the other one to RTSI4, and the IMAQ part to RTSI5. If the pulse is generated in RTSI2 then IMAQ should point to RTSI2 as well.
Check this suggestions you might find them useful. Good luck!
Nestor.
Nestor