The guys at work have been listening to my tunes via WinAmp & Hijack since you got it working a few days ago and they haven't reported any cutting off of tunes or any other odd behaviour. However I'm pretty sure I've got

[Startup]
ReserveCache=8

in my config.ini already. Maybe that's why I haven't experienced any problems. Mine's also an Empeg MkII.
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Marcus 32 gig MKII (various colours) & 30gig MKIIa