When using crossfading from a track that 44,100 to a
track thats 48,000 the track track will cut off a few
seconds early rather tha crossfading. This is when
using the winamp2 plugin with Media Jukebox, so I
imagine it is the same with winamp.
Not sure if we're still maintaining the winamp2 plugin, but follow up on the flac-dev list at xiph.org if this is still an issue for you.