What processor are you running? It sounds like you're talking about a CPU power connector. The processor may not be getting enough power with just one 4-pin connector. It is recommended that both slots are used on motherboards requiring an 8-pin connector.
Does your power supply have other 12v ATX 4-pin connectors?
Many motherboards come with 8pin connectors for the CPU but like in your situation many motherboards only provide 4pin. I am using the same 4pin on a 8pin motherboard without any problem. So you don't need to worry about that. Just place the 4pin connector in the right place and if I am right the in top 4pins.
If your computer still doesn't boot there must be a problem with other components in your system like ram. Please try this and report back.