Does sound like a driver issue. Are the clips repeatable? (As in, when you rewind back to when you heard a clip, does it happen again). Do the clips occur even when you turn the amp down to a low level? Do the clips occur when you turn the amp up, but the levels downs in your software? This might help determine if it's a clip from a actual overload, or if it's a clip from a buffer/driver problem.
Sometimes, video drivers, network card drivers, and motherboard (chipset) drivers could be the culprit. Might be easier to first test the signal line from your speakers to the computer, making sure it's not a hardware issue outside the computer. Are you playing the CD thru the computer. or is it playing thru a CD player?
Check your control panel for any AC97 soundcard settings. Look for entries other than 'Sounds & Audio Devices'. For example, my soundcard at my work computer has a 'Sound Effect Manager', which allows various EQ, sound FX, etc. Also, sometimes when you install a new codec pack, it changes the codec that is being used for playback, applying different settings or filtering, or creating new control panel entries. May be as simple as going thru the settings & removing everything not necessary.