Any chance you have a front audio connector on the board, and the cable connected to the case uses a different pinout? (HD vs. PC97) You might not notice a mismatch until you plug something into one of the jacks.
Check the BIOS setting for the front audio (if there is one)
If you're using something other than the basic windows drivers, check the software's jack configuration. Some driver sets have utilities that let you reassign the ports for different speaker configurations. (This is unlikely to be the problem, because green is almost always front left and right, even if the other jacks are switchable)
Also, look in the motherboard manual and see if there's a jumper to enable the jack instead of the speaker. My Lenovo desktops autoswitch like a laptop would, but it's possible that yours uses a jumper.