I think at this point they were selling their image processing systems to intelligence agencies like the CIA and NSA.
IIRC, the NSA bought a lot of NeXT systems, and he had to get a clearance for that too. Or maybe this was the same clearance.
People often assume that clearance is only given out in rare circumstances. It's surprising how easy it is to be told you need it and often when you're dealing with certain agencies it's easier for them to make sure you get it so that if they say the wrong thing then they're covered by your arrangements too.
yep Pixar must have been on the USAs equivalent of List X