Definately Vertex Buffer Object that solved it. I've still got
Framebuffer and Buffer swapping still checked.

Lighting []
Sync to VBlank [X]
Texture Compression []
Framebuffer Object [X]
Vertex Buffer Object []
Always use buffer swapping [X]

Is my current setup, if I check the VBO option the flickers return.

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https://bugs.launchpad.net/bugs/1070275

Title:
  [fglrx] Unity flickering on window updates with fglrx and VBO enabled

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