In batch mode, javac uses a caching impl of FSInfo. This is handled in javac Main here:

            boolean batchMode = (options.isUnset("nonBatchMode")
                        && System.getProperty("nonBatchMode") == null);
            if (batchMode)
                CacheFSInfo.preRegister(context);

There is no corresponding facility within the JSR 199 API (JavacTool/JavacTask etc) meaning that we never cache fsinfo when JSR 199 is in use, except in the trivial case where 199 delegates to main (i.e. when a simple run is called.)