jdk/make/javax/Makefile defines both SUBDIRS and compiles .java files via AUTO_FILES_JAVA_DIRS. There is some interaction between the 'all' target defined in that Makefile and the one defined in Rules.gmk that causes each subdirectory to be entered twice. See build log for an incremental 'gnumake' in jdk/make/javax attached.
The easiest fix would be to move AUTO_FILES_JAVA_DIRS into its own Makefile in an 'other' directory and have javax/Makefile just have an subdir loop, including the 'other' directory. That would allow also for a better clobber build of the sources in AUTO_FILES_JAVA_DIRS.