Do you have vista?
I have this happen to me when I reinstall SH4 on my vista64 computer. I fix it by going into my graphic card's options and disabling all advanced options like anti aliasing, forced mip maps, multisampling, threaded optimization, triple buffering, etc. I then run the game and it starts up fine. I make sure I set the resolution I want in game and then exit, reset the graphics card options, and then run SH4 and everything is fine.
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