uname -a is answered 'FreeBSD ... 6.3-RELEASE FreeBSD 6.3-RELEASE #2 ... root@fc:/usr/src/sys/i386/compile/VKERN i386'. This looks like a 32-bit kernel, right?
When I build without -Duse64bitint, Configure makes dependent directories named 'i386-freebsd'. With the switch, Configure says it's going to make directories named "i386-freebsd-64int". This seems like 64 bit ints are not the default. Or did I mistake your meaning?