I don't have any of these problems your talking about so I guess were on different pages of the universe. :) Ive been using Java on my Linux Suse distro for 4-5 years and Ive never had a problem installing the software. For someone who develops with Java it is important to me that my app(s) will run on Windows as it runs on Linux, and they do. So the cross platform compatibility is a plus for me. I don't know if you pay much attention to what goes on in the Java world but there definately is work going on to provide better integration with the native platforms. You can look at the JDIC project for example.
gotta run! leouser