Understanding some things that may or may not be weird (I don't know.)

Hey guys. I'm working on a small time project for fun and running into a small snag that maybe everyone on the internet might be able to help out with.
So, I'm working on a project to create an arduino controlled power switch for my computer. The switch itself should be a simple task and then I can add fun stuff like bluetooth later.
Here is the problem. I can't get the simple part to work. Now, I know that the power switch for a desktop is a momentary action switch and all it needs is a closed circuit for a fraction of a second. So, what I did was write a small piece of code to write high on a digital pin when there is a button press and hooked it to the input and ground of my motherboard power pins. Nothing. Doesn't react to button presses. Here is the interesting bit though. If I hook the two pins on the motherboard to any pins on my arduino with or without power to the board, it triggers a signal and turns on the computer. It even worked with ground to ground. Can someone explain that to me? It is also important to note that the arduino works fine. Was able to create button presses to turn on a simple LED just fine.
Any help would be nice.
Thanks a lot!

Never mind. I think I figured out the problem. The problem is that the two pins on the motherboard are supplying power because of the PSU in the computer. It's basically like there is already another voltage source. Thus, I think I'll have to use a relay to do the job. Else the arduino just gets bypassed like it's a wire.