Hello,
It will depend on how you are doing the data acquisition. If you are doing independent loops it should work fine because they will be running in different threads.
If you are using LabVIEW, you can even do two separate subVIs to force LabVIEW to run in multiple threads.
I would suggest you to try two independent VI or programs and test them one by one. Once you have that then call the two VIs or programs from your main application.
Hope this helps
Ricardo S.
National Instruments.