In certain cases, the program was making itself "topmost" window so that if a dialog window popped up (i.e. the Options dialog), it would be below Media Center and not visible. Media Center would appear to be totally unresponsive.
We've fixed this issue for tonight's build, so please test it out. It's possible there are other window "focus" issues remaining.
If problems remain, please try to figure out a series of steps that reproduce the problem so we can try it here.