You can't do anything about the flickering because it's a known issue. Maybe it'll be solved in the next Project64 release (in 2008) or use a 3rd party video plugin.
About the box thing, if you have integrated graphics, you're fucked. You need a DirectX 8 cappable graphics card in order to correct some graphic bugs. A DirectX 8 or DirectX 9 card along with Jabo's Direct3D8 will do miracles.


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