I understand that the code was developed by someone else so it will be more difficult for you to troubleshoot it. I would like you to try running a couple of examples to see if you can acquire all of the necessary data. Since you are using an S series board, you now have the option of using DAQmx as long as you have LabVIEW 7.x or later. Here is a link with some of the Advantages of DAQmx: Here is the link to a DAQmx Example that you might find helpful: NI-DAQmx: Acquire N Scans Using an Analog Reference Trigger.
If you still must use Traditional DAQ, please try this example: Acquire Analog Input Data Using a Hardware Analog Trigger.
I hope that you find this information helpful.