I know about this 'problem' but have no solution for it. As you say, it's not a big deal. IT has to do with the way the update script restarts itself using batch files and such. If you look carefully, what actually happens is the client restarts, but your keyboard goes to another DOS console superimposed on the client!
So you can type 'dir' and it'll work, and the client keeps going too. weird, eh? So you can also type 'exit' to exit this phantom shell, and the client keeps going. Then when you hit 'q', instead of going to the phantom shell, the client sees it, and exits normally.
I suspect this may actually be some weird bug in Win2K's DOS batch processing or something bizarre like that. If anyone is a guru on DOS batch files, please contact us and maybe we can figure it out...