It is difficult to know the exact source of the problem since you should be able to trigger both devices simmultaneously. Since you are performing AI on two separate devices, you will need two separate AI "circuits/paths". You will need to call AI config to generate a distinct refnum for each device, and you will need to perform AI Read for each device in your acquire loop (this means you will have two AI Read VIs in your acquire loop). Take a look at the examples for multi-board AI (distributed with LabVIEW) and notice the multiple calls to AI config, AI Start, AI read, AI Clear. You should be able to notice how the "data flow" before, in the acquire loop, and after is sequenced by the error cluster wires (you call AI Read twice - once for each device refnum). Now, th
e same logic applies for writing to two separate files. You simply call File Open twice outside of your loop in order to generate two distinct file refnums. In the acquire loop, wire the output from each AI Read to a different Write VI. At the conclusion of the loop, wire each file refnum to a distinct File Close VI (there will be two). As with the acquire logic, the sequencing is determined by the error cluster wire.