Okay, I've got something for you. Deleting lines 98 to 104 of core/com/limegroup/gnutella/DownloadManager.java solves the bug.

Runnable checkpointer=new Runnable() {
public void run() {
if (downloadsInProgress()>0) //optimization
writeSnapshot();
}
};
backend.schedule(checkpointer, 0, SNAPSHOT_CHECKPOINT_TIME);

Those lines cause all the trouble.