Check client_connections_delay in downloads.ini - should be 180.000000 .Thats the default anyway.If you use a shorter delay you might get kicked out.There are a lot of different versions out there and some might work better or worse - in short it is a mess.
emule worked ok for me with a winme partition under wine.There is a page about how to setup emule without a win partition at
http://www.linuxi.de/p2p.html
But that is in german and didn't work for me so far but that might be a problem with my system.