This is an issue with NI-488 versions prior to 2.0. If you have a PCI-GPIB, USB-GPIB, or ENET-GPIB controller, then I suggest you go to ni.com/downloads and get the latest NI-488 driver.
The newer versions have a better definition for how multiple processes affect (or do not affect) each other. Specifically in your case, taking a board offline in one process will not affect board-level functionality in other processes. (Prior to 2.0, it took the board offline globally, which is what you are seeing.)
The problem you are seeing is specific to NI-488. If you mix and match NI-488 and NI-VISA programs, you may see the same symptom, since NI-VISA uses NI-488 for its GPIB functionality. However, if you are using just NI-VISA, you would probably not see thi
s symptom, since we have worked around this issue by ensuring that we never take a GPIB board offline if any other VISA module or process is using that same GPIB board.
Also note that each driver potentially has its own set of bugs. So while I would not expect it anywhere else in NI-VXI or NI-VISA, I cannot guarantee that.
Dan Mondrik
Senior Software Engineer, NI-VISA
National Instruments