Found the problem, I had TeamViewer 7 open. It has a feature called 'QuickLaunch' that tries to embed a button in the top of the screen to quickly share that window with someone.
To disable it go to Options -> Advanced -> Show Advanced -> The second line down it says, Quick Connect Button go to Configure and either disable eqgame.exe if you like the feature or just disable it completely.
Hope this helps someone as I was raging for about 4 hours :p
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