I too am having this problem.  I have noticed that it is almost instant
from turning synergy on to the mouse not working properly with VLC.

This is on:
Ubuntu 10.04
Synergy 1.3.1-6ubuntu1
QuickSynergy 0.9-1

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Using synergy vlc fullscreen menu doesnt come up
https://bugs.launchpad.net/bugs/619066
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