Created attachment 2015
patch to correct problem
In focus-follows-mouse mode, a request to raise a window to the top should not move focus to that window (unless, obviously, it contains the pointer.)
I agree this problem is annoying me aswell.
Can you please document the repoducer, ie how you raise a window?
I encountered this problem when using the NEdit text editor. However, the current release version of that editor (5.5) has a bug that will interfere with reproducing this. So perhaps you can reproduce it with firefox instead. If you issue the command "firefox http://bugzilla.xfce.org" it should open the URL as a new tab in an existing firefox window (assuming you have an existing window) and raise that window if it is obscured by any other windows. However, focus should not leave the xterm in which the 'firefox' command was typed.
Created attachment 3039
Patch to fix 4.6.2
Problem still exists in 4.6.2.
fixed in master.