I have never seen an 8800GT with two PCI-e power connectors to even plug those into. Does yours? Sounds to me like they gave you an extra adapter.
I looked at the card and it really does have 2 PCI-E power connectors, that's the first GT I've seen like that.
PCI-E and PCI-E 2.0 supply different amounts of power through the slot. I would imagine that if you have a PCI-E motherboard you will need both plugged in but if your board is PCI-E 2.0 you should only need one. Each adaptor needs both molex connectors plugged in and the connectors on each adaptor should be on seperate lines from the PSU. Also each adaptor should be on a seperate 12v rail. If you are unable to connect it correctly you need a new PSU.
BTW I have about 10 extra molex connectors so it looks like your PSU is a bit weak.