How do you input your individual? It's possible to create a GP individual from the text representation of it? I think it is as I've seen in the javadoc files some methods wich read a gp node tree.
The way I do it is in the Evaluate method I use a modified "ECJ to Java" to generate java code from the individual and write it out to a java file. Then I compile the java file to a class file and copy it into the appropriate folder and call a function in a library that executes the code and calculates the fitness. The fitness value is returned back to the Evaluate method.