bin/jruby -v
jruby 9.0.0.0-SNAPSHOT (2.2.1) 2015-04-01 dc85f30 OpenJDK 64-Bit Server VM 24.76-b04 on 1.7.0_76-b13 +jit [FreeBSD-amd64]

I don't have a FreeBSD instance handy. Can you run this again with -Xbacktrace.style=raw and gist the result? We do use native calls to chmod...perhaps this is another case of FreeBSD having it in an unusual library?

https://gist.github.com/bgalbrecht/d0e9c7d1a475089f2646

chmod is in libc and the api is:
#include <sys/stat.h>

 int
 chmod(const char *path, mode_t mode);

 int
 fchmod(int fd, mode_t mode);

 int
 lchmod(const char *path, mode_t mode);

 int
 fchmodat(int fd, const char *path, mode_t mode, int flag);

where mode_t is defined as an unsigned 16 bit integer:
/usr/include/sys/_types.h:typedef __uint16_t __mode_t;

Ahh well if mode_t is 16-bit uint that could explain it. jnr-posix, through which we call chmod, currently uses a 32-bit signed int (Java int) for the signature.

Hmm... well we do have a test for fchmod in jnr-posix and that appears to be passing just fine.

If you would like to help move this along, a test for jnr-posix's chmod would help us determine if the problem is there or in JRuby's use of jnr-posix's chmod.