I found the problem with this.
It turns out that I was checking the project out from our CVS repository into a new project using the CVS Repository Exploring perspective.
When doing so, appearently the project is not “classified” as anything. Since it is not a Java project the “Mark Occurrences” does not work.
The only way I found to identify this problem was when you right click on the project and go to the properties page you DO NOT see “Java Build Path”, “Java Code Style”, “Java Compiler” and “Javadoc Location”.
To fix this I deleted the project and all the files in the project folder. Then went back to the CVS Repository Exploring perspective, did a “Check Out As..”, then “Check out as a project configured using the New Project Wizard”, then eventually selected a “Java Project’.
Now everything is fine.