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Somewhere in GSdx config on linux is an option to disable separate shader or something(I forget what it's called). I know gregory is always asking people to try that. So you might try it.
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Do you have any backtrace with Catalyst/GSdx configuration? Try to remove GSdx.ini and reconfigure it.
@Blyss, actually it only impacts the rendering quality.
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FGLRX package in Ubuntu is quite old, as in, about a year old. Numerous changes have been made since then. Have you considered manually updating to the latest Catalyst (as in, from the AMD site)?
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Glad to hear it's working man. How come you have on AA though? You should be able to turn it on by clicking on putting a checkmark on 'Enable HW Hacks' and clicking on 'Configure'.
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Oh I see. That sucks. BTW I totally meant to say 'How come you have no AA though?' lol.