The game runs a lot slower in Linux then in windows. For example when I select a unit, it takes the game a little while before it responds with the actions I've made. I've tested it in windows xp on the same machine and it is nice and snappy, everything works fine, I have also tested it in wine and it works just as fast as windows xp. So I'm thinking it's a platform issue.
Other stuff I've done is unpack the windows version and run it with the command 'java -jar proto.jar' and it performs just as slow as running the web start version.