Guess I found the answer on Logitech website:
Quote:
There are three main causes of pops and clicks:
Sound Card Many pops and clicks are created by the sound card. There are two common causes: sound card quality and older or mismatched drivers. If the overall volume level of the pops and clicks goes up and down as you change the volume on the speaker system, the noise is being generated by your sound card. Lower quality sound cards don't include the necessary circuitry to cleanly remove noise from the sound output. Logitech's higher-powered systems, such as the Z-560 and Z-680, are also sensitive to the overall quality level of the sound card. If you are using an older or lower quality sound card, we suggest upgrading your sound card.
The other primary cause is older or mismatched drivers. Make sure you are using the latest drivers for your sound card.
Multi-tasking If you are running more than one program on your computer that accesses the sound system at the same time, small pops and clicks can be common. This is a function of your computer and/or sound card. A common example is using a program that generates occasional audio feedback (such as beeps or other sound effects) while listening to an MP3 track in the background. The solution is to turn off audio feedback in the first application so that the background MP3 track is uninterrupted.
Interrupts in the Digital Bitstream On digital systems, such as the Z-680, it is normal to hear a very faint "tick" when you switch between inputs (by pressing the input button). You may also hear louder 'clicks' or 'pops' on a device such as a standalone DVD player or a sound card if it is plugged into one of the digital inputs. On some systems, this noise may occur when skipping tracks, switching audio streams (for example, from Dolby Digital to DTS), or navigating a DVD menu. The clicks and pops occur because the device is sending out an interrupted digital data stream. This behavior generally occurs with older software and older players, but is uncommon on most modern equipment.
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My sound card is SB Audigy, could it be a driver issue? It says my driver version is 5.12.2.252