Some slowing is to be expected when you're running two programs as opposed to one. How much slowing is happening? How much memory does your computer have? What kind of processor? What version of LabVIEW? What version of NI-DAQ? What version of NI-GPIB? Upgrades to any of them might be the solution. Combining the two separate programs so that you can better manage resources could be an option as well. With so little information to go on, it's really hard to say much more.
