Then either you used the wrong plugs on the soundcard, the soundcard isn't set correctly yet, or you're playing something (game or music player) than doesn't support 4-channel sound.
If the soundcard has an analog 4.0-speaker mode it doesn't really know or care whether the 2 speaker sets are 2.0 or 2.1 (though it may let you set "small" or "large").
If it has a 4.1 mode, or if both of your 2.1 speakers insist on getting 3 distinct audio channels from the souncard (L, R, bass) instead of just L, R then you might have problems.