Hello,
If you can run each VI independently then what you can try to do is call this VIs as subVI in your main VI and force LabVIEW to run in different threads. To do this, you need to open the VI properties of one of the subVIs , go to execution form the drop down list and on Preferred Execution Systems choose another option instead of the default.
You did not specify if you are using NI-DAQ or NI-DAQmx. The differences is that NI-DAQ is not multithread so even if you are doing separate loops or you are forcing LabVIEW to work on different threads, the driver will not let you. NI-DAQmx on the other hand, is multithread.
Another option if you are doing with traditional is to create a Task with all the channels you want to read,so that w
ay the board will multiplex in a certain time all the channels in one same thread.
Hope this helps.
Ricardo S.
National Instruments