I tried a couple of different things to try and get it to stop the first being to disable window snapping, but for some reason that just didn’t work. Luckily trusty google was to the rescue and has provided me with a great fix for this silly problem.

I wish I could take full credit for this but I really have to thank TechBlog for this one.  The issue really comes down to a property of the wobbly window plugin called “Snap Inverted”.  Disabling this property gets rid of this annoying behaviour and makes compiz fusion work with windows properly. The steps for fixing this are rather simple, so without further adu let’s get to it.  These steps work with Ubuntu Gutsy, but should work fine with any Distro runing compiz fusion and having the compiz-settings-manager installed.

1. Goto System -> Preferences -> Advanced Desktop Effects Settings.
2. Scroll down to the “Effects” Section and Click the “Wobbly Windows” plugin.
3. Under the “General” tab you will see as your first option “Snap Inverted” simply uncheck the checkbox beside it to disable.
4. You are now done, close down the Compiz Setting Manager and enjoy.

I hope this helps anyone getting really annoyed with this behaviour.  Hopefully compiz will disable this property by default in upcoming releases.