Which version of Java are you running? I think this only happens with Java 1.6; don't ask me why Sun decided to break keyboard shortcuts. Can you use an older version of Java instead?
Hi, I don't think Sun is to blame here. The Arduino-IDE is the first app I have seen where shortcuts are broken when using the 1.6JRE. I'm using a variety of java-applications which use a source-code from JRE1.3 - 1.6 . All of them still work fine (keyboard-shortcuts wise).
I think this issue needs some attention in the short term. JavaRE 1.5 will probably disappear very quickly once the open-sourcing of Java takes off.
Eberhard