Thanks for the feedback. Yep, that's a small bugette in the 2.0 release. It's fixed for our forthcoming 2.1 maintainance release, which'll be free to existing customers.
We did consider making the panel dockable. I'll pass your comment on to the team. In the meantime, you can still leave the script window open whilst you click around - admittedly this is easier on a high resolution or multi monitor system.