I don't think the case would have anything to do with it, unless it was grounding out. Speaking of which, you did use those brass spacers to seat the motherboard, right?
Could be a bad powersupply, a bad motherboard, a bad CPU, a bad connection...there's a lot of things it could be.
Intel Q9400 | Gigabyte EP45-UD3P | G.Skill 2x2GB DDR2 1000 | XFX HD5870
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