Hi Stephan,
The compiler that is integrated in Eclipse will generate only Java byte code for a Java VM. Eclipse will not use the Java compiler that is included in the JDK that you reference in Eclipse.
To use Eclipse with Janet SE, you will need to use an external Ant Build file. You can use the javac compiler that is included in Ja.NET SE to generate code for the .NET VM (it does this by default) . So you can also use the compiler to generate byte code for a Java VM by supplying the -java option.
Dave