I'm suprised it's loading up on one connection. If you've tried playing games with just one connection it's probably horifcally slow/instable, if it even ran with one for long.
Midknyte is right, you must use BOTH connections on the 8800GTX, you can buy converters that will convert molex connectors into PCI express power connectors, if your power supply isnt powerful enough, then that poses as a bad problem.
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