Bizarre. I have done some testing, and excluding confusing Winamp by fast forwarding and rewinding in VBR encoded files, Winamp, emphatic amd xmms all agree to within a very small tolerance - even on long tracks.

Wonder what is configured differently on your machine?
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Rory
MkIIa, blue lit buttons, memory upgrade, 1Tb in Subaru Forester STi
MkII, 240Gb in Mark Lord dock
MkII, 80Gb SSD in dock