Hmmm.. Interesting, just launched ObjectDock and did testing... 
(Am on Vista Home Prem, but have seen error on XP too)
I'm actually thinking that the CHS window is not becoming "active" even though it's in the foreground.
Using hotkey v. tray icon R-click menu is the same.  And the effect is the same on the Prefs GUI or the Editor Window... 
I activate it and *can* mouser-over it and the moused-over buttons/menus *do* show the moused-over color-change, but clicking does nothing.  I have OjDoc set to display icons of open windows on the toolbar.  If I click the CHS icon, it brings the window the rest of the way fwd, thus allowing it to work...  (I can tell this is happening because I noticed the top window bar get darker, thus indicating that the window had not been "active").  I have a hunch this might be an ObjDoc bug.... 
Also, just FYI, tried it with the FARR Options window and the problems does not exist....

Just fyi:  If ObjectDock (OSX-style launcher) is running, CH+S will freeze if you access the prefs.  The pref GUI will show, but will be unclickable (buttons, toolbars, etc).
It doesn't realy matter to me though....  I've adopted FARR as my launcher in place of OD...    :D    -steve