Why are class files different size when compiling the same code in eclipse, and then with the eclipse compiler via ant?

I am making an automated build environment using ant to build a freshly checked out source tree using the same eclipse compiler that is used in eclipse. The problem is that some of the resulting class files are different in size than the class file generated by compiling within eclipse. Why is this? Is this ok, and to be expected? As prescribed I'm telling Ant to use the eclipse compiler, like:

<target description="compile project with Eclipse compiler" name="build-eclipse-compiler">
        <property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/>
        <antcall target="build"/>
</target>