Running the Gen TTL AO1 application all the time and then putting a small delay in its own structure in between the two pulse generator structures works! It makes sense to me now that the Gen TTL was just timing out when the highlight execution was running, since it is a more complicated vi...and that whichever was second was timing out without the highlight execution function. It seems there is a somewhat significant (ms) delay between when the Gen TTL programs are triggered and when the actual pulses are output, so that whichever is second will not work as the first generator is still using the hardware (or something like that). Hence, the delay between the pulses generators is necessary to avoid this sort of interference.
I'd like to thank everyone for their help. I think this problem is finally solved.
Libby
