Hi Adam,
Do you have Java 1.5 installed? If so, could you try updating to the latest version and see if that helps?
You can download it here: Java for Mac OS X 10.4 Release 5
Earlier versions of Java on the Mac required this hack to get the AWT stuff halfway working. The newer versions allow them to fully function, but only if the JVM is started on the first thread...
And in one of the upcoming releases, I will try to integrate Java based code editors and even a debugger, so that's why I changed it now already. I could go back for the time being, but maybe it is easier to just update Java instead?
PS: I renamed your post so others facing the same problem can more easily find it.