I usually run hg from the command line. So I frequently right click a project and choose Mercurial > Status to clear wrong flags.
I keep the Mercurial status window in sliding mode to keep it out of the way.
Frequently (but not always), after I run status, the window appears, not in sliding mode, but docked back into the main window, where I do not want it.
I'm guessing it's using Mode.dockInto(this) somewhere - don't do that.
*** This bug has been marked as a duplicate of bug 143300 ***