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Batch compiler, when specified through the -properties argument doesn't honour the javadoc enablement property - org.eclipse.jdt.core.compiler.doc.comment.support. It only honours properties starting with the string org.eclipse.jdt.core.compiler.problem. The solution is to also add -warn:+javadoc to the command line and may be this is good enough. However, I think it it won't be obvious to the users and better to be honoured.
I think -enableJavadoc is probably the option you also need, but it should work from the properties file. It should honor all properties starting with "org.eclipse.jdt.core.compiler.".
The proposal in bug 375366 should also work for this i.e. enable javadoc processing if any javadoc option is found in the .properties file *** This bug has been marked as a duplicate of bug 375366 ***
Verified for Eclipse Luna 4.4 M1 Build id: I20130805-0800