The OP stated first, it wouldn't boot AT ALL, but had spining fans and no video, it was a timing issue that is known about a couple of MB, the commels and the Epias. You have not mentioned what MB you are using. This was corrected. There is a resister that needs to be changed, either by the owner or with a swap of the PSU itself.
Then he claimed he was having "mysterious" rebooting of his MB AFTER the resister change.
So, now, since you stated IT DOES BOOT, but then you lose VGA, that is a DIFFERENT PROBLEM. See, his didn't boot EVER, but he has spinning and no VGA. You said yours booted. And, you are not having Mysterious Rebooting. Different problems
You have not provided anything about your system. Not the MB specs, CPU, peripherals, how you wired it, your jumper settings, NOTHING.
Now, start a new thread, post all the information you can (what is a "molex connector") and I am sure someone will try and help you, perhaps even me.