well, it doesn't seem to affect the main window (sorry, hadn't tried that..), but channel windows etc "on desktop" (ie non-child windows) appears to use the workspace area of the primary monitor to determine if they are off-screen. a window positioned (partially) off-screen will be moved as far as necessary to get fully visible again (an option to disable that would be nice, btw..).
in my case, the window is detected to be to the right of the primary monitor and is thus (although the window is fully inside the secondary monitor) moved so its right border is up against the right side of the screen, though it uses multimonitors properly for this task and actually moves the window further to the right so it lines up against the right of my secondary monitor. so it seems to be a bug in the off-screen detection only considering the workspace of the primary monitor - though not for the main window.
hope that's clearer, and assuming you weren't testing with "on desktop" windows before, hopefully you can reproduce it..