Sorry for not commenting on this earlier, but I have been travelling with work - building and commissioning plant rather than computing.
It is now possible to build libjava with 4 byte alignment on cygwin, as hash synchronization has been disabled for cygwin (in libjava/configure.host). I have tested this in both 3.1.1 (cygwin) and 3.2, but not for a couple of weeks.
