I've been noticing this in the last few days. On my Mk1 (beta 12) it doesn't seem to skip ahead as much as pause momentarily. The duration of the pause seems to vary, anything up to 0.5s.
It doesn't seem to follow any pattern and repeating the track won't replicate it, so I assume it isn't a problem with the encoding. (Just in case, all my .mp3s are encoded using VBR, most with AC2.1 but I have been trying LAME. The skip seems to appear in tracks created using both encoders.)
I have noticed it in the Mk2 as well, but since it's not in the car yet, I'm still listening to the Mk1 for longer periods.
Geoff
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Got one of the first Mark 2 empegs...
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Geoff
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Mk1 Blue - was 4GB, now 16GB
Mk2 Red - was 12GB, now 60GB