|Look in the BIOS screens for a drive setting called AHCI. You may be using an IDE compatibility mode now.|
If you have that setting then try enabling it and rebooting. Do not change the jumper at this time. If the computer boots to Windows then shut down and try removing the jumper.
If at any time you can't boot to Windows then backup to the original settings. In that case the only way to get the 3GBPS setting to work would be to either repair or reinstall Windows.
You understand that you probably will NOT see any appreciable speed increase.