Hi Paul! It's been a while since my last post here, time flies!
Here's my issue: i've been using Jaikoz for ages and always had it installed in my home directory in Linux. When you made it possible to have it installed in whatever directory the user wished it was great. However I now find that you include the JVM into the installer and that somehow has to be ran as root, otherwise it fails with permission errors (since a normal user can't write to /usr/share/applications by default).