A tricky one to explain, but I know a few people had it, and I remember thread where Noel was discussing it with us.
Anyway, I still have this problem in X3. Only on old X2 projects so far. It seems to be something to do with trying to use buses when the console is in the multi-dock and on the second monitor. Trying to use any bus controls crashes the whole program.
Has anyone figured out any pattern or workaround for this? It doesn't happen when you're first working on a project, crops up at some point, and then has a 100% crash rate from then.