There is an input to the DAQ Assistant labled stop. To do things the way you have them, the input must be wired to TRUE. Otherwise the second acquisition cannot run because the first one still controls all the resources.
Is there a reason why you do the two acquisitions sequentially. You can set up one DAQ Assistant to perform both acquisitions at the same time by having both channels listed in the same DAQ Assistant. I have attached a file that does this.
Randall Pursley