Strange sound when capturin in MPEG-2

Hi,

I have a HP Pavillion PC running Vista 64bit and ATI AIW HD video card which I use to capture video from a VCR source. Whenever I try to capture in MPEG-2 format there is this regular (0.5s-1s period), kind of clicking sound superimposed on the regular audio. Pretty annoying. It appears only in MPEG-2. If I try to capture in MPEG-1 or AVI , I don't have this problem. I tried Pinnacle studio 12.1 and Nero Vision and both show the same problem although the click seems to be louder when I use Pinnacle studio. It does not disappear if I disconnect the audio cables connecting the VCR and the computer. Looks like it is coming from the PC itself.
Any suggestions how to overcome it? Has anyone have similar experience before?
TIA