as elbenj said, if it's the same spot every time then the pop got recorded onto the audio. what kind of soundcard are you using? does it have the ability to sync to an external source? if so, make sure that either the soundcard or the external are set to master, but not both. normally, the external is set to master during recording and the sound card is set to master duing playback.
if that doesn't solve your problem, then go into control panel and check to see if your sound card is sharing an interrupt (IRQ) with another device. If so, try rearranging the cards in the PCI slots until you get the right configuration, because some slots on your motherboard are set to share IRQ.
FYI, I've found that using the ACPI configuration in Win2K is crap. It puts all your peripherals on 1 IRQ, and they do not play well together for me. your mileage may vary.