I'm behind a SOCKS-Server, too (university) and found out that not every client seems to work with Sockscap - usually I saw some hosts, but they quickly disappeared again. So maybe it's not your server settings but just the wrong client:
For me Bearshare didn't work, Limewire worked fine in V1.2, whereas the new version 1.3 does not and Gnotella only worked when I changed the portnumber to numbers around 8000. Hope that helps...