Not able to reproduce this yet, going to need more info. This is what I am running:
$ uname -a
Linux ubuntu12-x64-template 3.2.0-44-generic #69-Ubuntu SMP Thu May 16 17:35:01 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
$ gnome-shell --version
GNOME Shell 3.4.1
In the Configuration Editor, under org.gnome.desktop.wm.preferences, auto-raise is disabled, and focus-mode is set to 'click'. Are there any other options you have enabled that are non-default?
Is there a particular area that you passing the mouse over that is causing this (editor pane, tool window, menu/toolbar)? What emulation are you running? Could you export your SlickEdit options and post them? Also may need a look at at the restore info from your configuration directory (vrestore.slk) to get an idea of your window layout.