Anaconda has always had these tiny little message boxes when it is doing things
like reading the package list. They should be larger and more obvious. The more
chunky nature of the rest of the new theme, and the beta pop up make that even
more obvious now.
Are these the transient popups (with no user interaction) you're referring to?
We will move to a small wm in the next release to address this.
Added in CVS