Been there! Knoppix 3.8.3 did that to me for a fairly simple sound mixer, and 4.0.2 did the same recently for something else (I forget what). Since I'd only just wiped the machine, I let it carry on, on the basis I could just wipe again and start again.

In the event, it installed several hundred packages, and the only change I could see was that Kaffeine disappeared, and Rosegarden4 would no longer install. Not a big deal.

The Knoppix-installed machine is now the fileserver for the network and doing very well at that.