Thanks for the answer.
Since the package manager seems to handle dependencies well, I thought I would try the ultimate test. That is to install VLC with its hundreds of dependencies from the Ubuntu repo and see what happened!Apart from that, why are you upgrading the package lists? There is no need to. You are testing Precise Puppy beta4, which is built with the latest package lists.
The main precise repo has VLC 2.01 which is quite buggy, but the precise-updates has VLC 2.03, which is the current version.
There seems to be a problem with the package manager, though. Now that I have a lot of user loaded packages, it takes an infinite amount of time to do the package search. It worked OK to start with.
I treat installing .debs as a one-way ticket. So I'll delete the save file and start again!