You don't mention which motherboard you have (please do!) but the fact that the second pair of ports are located away from the first pair indicates they're probably connected to another controller. Enter the BIOS setup, I expect you will find an option for it somewhere under a menu called "Integrated I/O devices" or something similar. If you, apart from enable and disable, are able to choose "RAID", don't.
This might also be caused by a driver issue. You don't mention which OS you have but I'm guessing some version of Windows since it is the most common (telling us which it is would help). Have a look in device manager which you find under "system" in control panel and check if there are any devices marked with an X or an exclamation mark (at least that's what I think problems show up as - I don't have a Windows box handy). If so, and unless they complain about something that is clearly not SATA ports or devices, check the motherboard manufacturers website for drivers.