off the top of my head... i can only imagine a few things... ...one is that maybe the sub has an attenuation or volume setting enabled on it, to lessen the effect of the bass output... ...2 is that maybe an audio setting on your system is turned down, try reinstalling the audio drivers on your sound card, or resetting a software setting on your system... ...3 is that maybe some cabling is loose, so you might want to check to make sure all connections are secure, power connections and audio connections, on both your computer, and sound system... even try 'adjusting' the audio cabling around as a song is playing, to see if its not just the cabling that might be faulty, possibly... ...4 is that maybe the sub itself is going bad... hope not anyhow.
you could even try relocating the 2.1 speakers to a different computer (or other viable audio source) temporarily to see if that changes things at all...
...if it does turn out to be going bad, im sure you can take the 2.1 set back to the store for a replacement, if you still have the receipt onhand (depending on the stores return policy also)... ...if you purchased them online however, not too sure really... you might be able to get help from the manufacturer on it, such as with their replacement policy, or RMA service, if they have one... or from the online retailer you purchased it from, possibly.