My Command User Interface window undocks itself when I switch between commands or environments. I used the Solid Edge Options Helpers to toggle over to use docking window form and have docked to my Pathfinder on a second sceen. But, it is very unstable. I never had this issue with any previous version.
Window docking is recorded for each environment, and SE has a lot of environments. You need to dock the bars where you want them (or un-dock them) in each environment. When you switch from part to sketch and back to part all the windows should be docked the same in the part environment. They could be in different locations while in sketch. If you are experiencing problems with windows moving around within the part environment, then that is a problem that should be reported to your support person, VAR, or GTAC.
Thanks for the response, Jason. I have used this functionality with ST4 without a problem. After initial set-up all worked well, now that my company just upgraded to ST6 the windows just pop out with every environment change. It looks like I will be writing an IR on this.