Nobody out there? OK, in case anyone else has this problem, I realised that it was related to an upgrade from Mandriva 2005 to 2006. I found that with Java 1.4 the problem partially disappeared in that the splash screen didn't sit in the middle of all my desktops, just the desktop I started LimeWire on. Still unhappy with the 5 minute wait, I found the answer lies in changing the firewall options to "Do Nothing(not recommended)". I could download with this setting, but I'm not sure whether uploading was allowed, without adjusting the (shorewall) firewall to accept calls to the "listen on" port in that option.
Anyway, back to normal, now.