OK, just installed Opus freshly on a virgin installation of Windows 7 Professional.
For the X-Mouse setting (but without the annoying auto-raising of windows), see here. Log off and back on to activate the setting.
Afterwards, program windows generally get focus (but do not auto-raise) just by hovering the mouse over them.
Now note that if Windows Explorer is in the background (and partially covered by another window), you can still do all sorts of things with files and folders like clicking, dragging etc. without Windows Explorer jumping in front and covering up your foreground window. This is very useful for drag-and-dropping files or folders from Windows Explorer to your foreground window. Only if you click on the titlebar, on a column header or into an empty area of Windows Explorer, Windows Explorer will jump into the foreground since in this case, it (correctly) assumes that you don't want to drag files out to a foreground window.
Now try the same in Opus. You can't do anything in a Dopus window (that is in the background) whithout it instantly jumping in the foreground and thus annoyingly covering up the possible target of a drag-and-drop action.
This happens instantly, and actually has nothing to do with Direct Folders or Filebox Extender. (It doesn't happen instantly if instead of the above Registry setting that other tool TXMouse is used. But it happens after a while and then it's just the same problem. Anyway, we can leave TXMouse out of consideration since the problem is present also without it.)
Regards David.P