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?
Yes
We will move to a small wm in the next release to address this.
Added in CVS
closing