I deleted all tracks (after refs=0), resynced, created two playlists and added around 50 tracks in each. In the middle of syncing I got the exception again. The stacktrace is: (dont know how to alt-printscreen in OS X, so am typing it out myself)

java.io.IOException: Timed out.
at org.jempeg.empeg.protocol.ProtocolClient.waitForPlayer(ProtocolClient.java:623)
at org.jempeg.empeg.nodestore.PlayerDatabase.readOnly(PlayerDatabase.java:1594)
at org.jempeg.empeg.nodestore.PlayerDatabase.synchronizeReadOnly(PlayerDatabase.java:1408)
at org.jempeg.empeg.nodestore.PlayerDatabase.synchronize(PlayerDatabase.java:1356)
at org.jempeg.empeg.emplode.EmplodeSyncManager.synchronize(EmplodeSyncManager.java:155)
at org.jempeg.empeg.emplode.EmplodeSyncManager$1.run(EmplodeSyncManager.java:119)