I believe the libjava Makefile.am on the gcj-eclipse branch has a bug with -j builds, where it may try to build the CNI header files multiple times.
-- Summary: [ecj] libjava Makefile has -j bug Product: gcc Version: 4.2.0 Status: UNCONFIRMED Severity: normal Priority: P3 Component: libgcj AssignedTo: unassigned at gcc dot gnu dot org ReportedBy: tromey at gcc dot gnu dot org OtherBugsDependingO 28067 nThis: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=29278