Ok I did some digging around.
I found out that I have to issue the following to make sure Sun's version of Java is being used instead of GCJ:
update-java-alternatives -s java-1.5.0-sun
Then make sure that in /etc/jvm that the following line is on top:
Then in /etc/eclipse/java_home edit the file and make sure the following line is on top:
The above applies to ubuntu but it should work for most 'endians.
HOWEVER, this didn't really stop the error. Eclipse still says it cannot resolve java.util.Scanner.
Thanks again for any help,