Check our what soundchip you've got on your motherboard and update your drivers.
Go into your driver and go to preferences or w/e and select the correct devices for everything plugged in. It might be that your mic-in is a flexijack that'll pick up sound from your card if it's in 7.1 mode so check to see if it is, if so change to 5.1.
If the problem persists, take everything out, and plug it in one by one. If your driver is anything like mine (SoundMax) it'll say that a new device was connected and you can select what it is. But my guess is that you're in 7.1 mode and your mic-in is used as an output.