I might know what your problem is. I reread your first post a few times and if I understand you correctly you don't encounter problems when you have Metacity running. Now based on Wikipadia Metacity is default Window manager used in Gnome 2 Desktop enviroment but it was replaced with Mutter in Gnome 3.
http://en.wikipedia.org/wiki/Metacity
http://en.wikipedia.org/wiki/Mutter_(window_manager)
Cinnamon uses Muffin which is a fork of Gnome 3 Mutter Windows manager.
http://en.wikipedia.org/wiki/Cinnamon_(software)

So all of your problems might be the result of changed default Window manager which probably requires a different code to work.