I don't know how else to say it. Changing the trigger source should have no affect on whether you have one or two channels acquired. That is not how a scope works. I don't know what those images are supposed to mean. What is your input to both channels? If you are inputting a square wave to both, then you have a problem acquiring channel 1 and channel 2. There are two different scope captures there and who knows which is correct?
The LabVIEW code you posted is poorly written and without the actual device, next to impossible to debug. The Call Library Function Nodes make it even more difficult. The code comes from the vendor and not NI. You need to talk to them.
