First of all, for the font properties thing see the font properties section of the java release notes and download the revised font.properties file:

http://java.sun.com/j2se/1.3/relnotes.html

The MetaCtrlInsert mesasge is (I think) a Swing problem (Swing is a group of classes to make purty GUIs in Java) and it won't cause you any trouble.

You shouldn't be getting a segmentation fault. ;) Not sure what's wrong there. You may have more than one version of Java installed and an older one is running. Open and terminal and type:

java -version

And make sure that the version information is for Java 1.3.1. If it's not then you have older versions of java or Kaffe installed as well. (Kaffe is an open source implementation of java that mostly implements Java 1.1). Remove those if they are present.

Give it a try anyway.