After trying the other suggestions posted here without any luck, in the end we implemented Dennis' solution. We managed to find an old PC and went back to the old card.
If you are interested:
-the old card was the same one pictured in the other thread, but the 1.6 version didn't help.
-enabling DOS in MAX also didn't get us any further
Jason: We had communicated with a Varian rep about using the NI USB with our setup, and he was certain it would work, but it seems Dennis is right that it requires a newer Varian software version than the one we have. When starting up the Varian software, it just give the notification that "No IEEE card was detected in your computer" and we can't get any further than that with the USB in place.
Thanks everyone for taking the time to help us out! Very much appreciated.
Is it possible to get the newer version of the Varian software that will work with NI-488.2? Using old computers is only a good solution as long as you can find them.
Very good point Jason. We'll try and see what we can do to solve the problem (and it seems getting the software updated would be a good place to start), but using the old PC buys us some time, so we can keep analyses going.