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Loss of Synchronization for Finite Pulse Train generation

I have successfully generated a finite pulse train on my 6608. My program is based off an example I got from NI Zone (Square_Wave_Trigger.zip).

Unfortunately, the Finite Pulse Train loses synchronization every once in a while, and I'm not sure why. Is there anyway to prevent the loss of synchronization???

When I say loss of synchronization, here is what I mean exactly. I'm generating 4 pulses, but every once in a while, when I reprogram my equipment, I lose those 4 pulses. They seem to go out of phase or something.

I have included my code as well (Sync.txt), which is slightly different from the example code. In my code, the finite pulse train is generated by the "Sequence Gating Pulse"
and the "USIP Firing Sequence" lines of code, which are clearly marked.

Any help would be greatly appreciated. 😃
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'Loss of synchronization' is still unclear. Do you lose the pulse train, never to return, or just occasionally? What happens when you reprogram the equipment; do they clear or assert rigger lines?
I'm thinking that you may have a situation where you are sending a trigger in the middle of a pulse generation sequence and missing the trigger.
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I lose the pulse train until I reset my counters. The pulse train shifts out of phase with the main pulse. It's easier to see in the pictures below.
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