Selecting a brush, or a content aware healing brush, causes the program to freeze-up for a noticeable period of time, over 30 seconds, and often, only unfreezing by clicking a different tool, then coming back to the brush.
Have you installed all the updates for Photoshop CS6? You should be on 13.0.4 or 13.1.2.
And while we've seen reports of lockups like that, we haven't been able to reproduce them, and strongly suspect that something external may be interfering with event processing (sending events to the wrong window). One of the common suspects seems to be the Chrome browser (closing it eliminated the problem for several users).