Without seeing your code it would be hard to give specifics, but does -5.2V appear anywhere else in the system? One possibility is that you aren't looking at the channel you think you are.
How much delay is there between when you tell the scope to begin acquisition and the read occurs? Could the read be getting its data before the scope actually triggers?
What happens when you run the "Fetch Waveform" vi by itself? In other words, if you setup the system and generate the trigger manually such that the proper waveform is on the scope, does Fetch Waveform run by itself return the proper result?
If this is not correcct there is something basically wrong with the function for reading the waveform. Again, giving specifics are hard, but open the VI and go
through it statement by statement making sure that the settings and commands make sense for your application. Many vendors make excellent instrumentation, but I have yet to see one that could write a good driver.
Also, could you describe what the proper waveform looks like?
Mike...