Same thing here: last chunk is not prioritized and - until RC2, the other chunks were downloaded in a "left to right" fashion. With RC3 things have changed, and chunks come randomly, it seems. I took a look at the .emule configuration file, and found no trace of the "First and last chunks first" option. Is this the problem? If so, could one manually add the entry and how should it look like? If not so, I hope to see it fixed in next versions.
And by the way, thanks to all devs for their work!
