I'm using Ubuntu 12.04.1 LTS i586 and decided to upgrade to 4.1 to take advantage of the new multicopter features. I didn't read my email before doing the upgrade which would have saved a lot of time.
When I started the sim using my old HeliX.jar from the previous version the programme would only start as v3.1. I spoke with support and they promptly and kindly explained the 4x release now requires a license code and the previous method of copying Helix.jar is now redundant, this was all explained in an earlier email from them.
Anyway, I checked my email, entered the provided key and now everything works just fine. With Ubuntu to overcome the dsp sound issue you need to start the programme using
./runHELI-X_sound_padsp.sh.