I have yet ran into a module that didn't work in a pure CSS skin. NOTE: they were not xhtml compliant nor CSS based, but they all worked and without any huge issue. I think the worst issue I have ran into with Pure CSS skin / containers and modules is sometimes the actions.print / RSS / Add pieces show up a bit lower then I want in FF vs IE.

I personally prefer pure CSS skins as I find they are very easy to modify and once you get the hang of it are much more SEO friendly, and smaller. I can create a complex skin in about half the space as a table based, and as web 2 tries to phase in more and more. table layouts will go away slowly, so its a good thing to learn how to do CSS skins.

I do agree it can be very very frustrating to get things just right but once you get the hang of it and build a few skins, you will be coding CSS skins faster then table based ones.