This is very strange. You could change the content for the RadTransitionControl even when the animation is not over. You could easily try this in our online demos - http://demos.telerik.com/wpf/Telerik.Windows.Examples.xbap?TransitionControl/FirstLook. We are not aware of such problem with the control, it could be a issue related to the PRISM.
I would suggest you using a RadBusyIndicator to notify that something is processing. When the operation is complete, you could hide the RadBusyIndicator and place the View in the region(RadTransitionControl). In this scenario, you won't need to change the views in the region and I guess the problem will go away.
I hope this helps.
All the best,
the Telerik team
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