New beta is up. Should fix the latest problems, though the QuickCapture bar is temporarily non-functional while I improve it.
One thing has changed. In the previous betas i had added a feature that would try to find a *CHILD* control region to select as the active area if it would have otherwise selected nothing and the option was enabled to select the active region (see cmpm post above).
That is, the "Auto Select Active Window" option was falling back to selecting an Active CONTROL of the active window if you just grabbed the active window.. I've changed this now to be an option, disabled by default, which you will find in the "Window Capturing 1" tab. So if you liked that new feature, you can go enable it from there.
The only time that would really be useful is if you want to automatically select specific sub-regions of windows for performing effects on them (like making them glow, etc.).