First of all you don't need the flat sequence at all. The movement of data along the wires will dictate the execution order. No code, section, subvi, function, loop, etc will start to execute until all of its inputs are present. Usually the error wire is sufficient for defining execution flow. Remove the sequence, but not the code in it.
In the loop (frame 2), the DAQ is always writing the same data. I don't think this is necessary. Just write once. Your architecture to do this is not correct. Inside the loop, you should have one big case structure. Wire the Collect Data 2 button to the case selector. In the false case, do nothing but pass the error wire and the DAQ task wire and the 2D array wire. You should use shift registers for the error and task wires so that the info gets propogatd from one loop iteration to the next. Ohterwise you will lose any error info from one iteration to the next. In the True case, you will need a flat sequence. In the first frame, put the delay. In the second fram, put the DAQmx write with the proper data (no extra case structure needed here). In the third frame, put another loop to wait for the Collect Data 2 button to go false. Again put a case structure. Use a local variable of the Collect Data 2 button. In the True case, just pass the shift register wires. In the False case, put another DAQmx write with the proper data. Put a True constant and wire it out of the case and the loop and the sequence to the outer loop stop sign. If I described it right, the first loop will wait for the button to go True. Then the DAQ will write after a delay, then the next loop will wait for the button to go false. After the button goes false, the DAQ will write again and all the loops will stop. See if you can figure out where to put the DAQ Assist and the rest of that code. Instead of using a Value property node, use a local variable. Its quicker. Beware of race conditions.
Re-write the code as explained and post it again.
If the unit fails self test, and another one fails also, you must be doing something to abort the test. Don't worry about it unless your new code doesn't work.
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