Hi,
I'm not sure if I got your question. You have a VI that communicates with a GPIB device, using the GPIB-PCII/IIA. And you also have a PCI-6035 to perform data acquisition. Is that right?.
When you run the two toghether you notice a slow down. On which VI?. How much slower?. It is difficult to provide suggestions without more information.
DiegoF