Try starting it from xterm. Open xterm (or eterm or whatever terminal emulator is your favourite) change to your LimeWire directory and start it by entering "./runLime.sh"

If you start it from konqueror or nautilus, it's very likely that it sets the working directory variable to /, so java doesn't find the libraries since the runLime script does not contain the absolute path to the .jar-libraries.

(As an alternative, you could also edit your runLime script).