I've noticed that users simply do not understand multi-select boxes. Even the software developers using my test platform at SciPy.org (these are smart guys--mostly PhDs of some kind of deep science) don't get it until explained. They see the list of Subversion repositories, for example, and assume those are the ones that are selected. It's happened with both of the domain owners, specifically in the Subversion list.
These types of lists occur throughout Webmin, and it's probably not the time to be ripping out and replacing them all, but it is definitely appropriate to have popup help (I'm working on the help for all Virtualmin options, should be done before release), and it's probably appropriate to relabel it to indicate that they need to do something to make those listed repositories actually enabled for the user. Same goes for anywhere we use a multi-select list box.