Iamyourzero:
I think this problem stems from the newer version of Winamp, not you OS, mobo, etc. I had a similiar problem (the skipping ahead, not the scratces and pops) and it turned out that the version of Winamp I had (2.71) had a problem with files encoded with a certain codec.
My advice:
a.) Comb Winamp.com's message board and try to find a patch (that's what I did and it works fine now).
b.) Try to find an older version of Winamp and see if that corrects the problem.
c.) Use Sonique.