Verify and defrag your steam cache for the CK and Skyrim. Mine does this sometimes and that usually fixes it. Otherwise, reinstall the CK. It can get a little weird sometimes...
Probably something about Steam cloud and going back and forth shutting down/running CK and Skyrim all the time. I tend to click "cancel" in the preparation window and try again once or twice, it usually makes the CK launch normally.
If this happens after runing Skyrim, while testing or something, Steam is probably synchronizing the savegames. It happens to me sometimes. Just check the Steam icon when this happens, and you'll see it's syncing.