And it works on trunk/1.1?

1.0.x seems ok with Java 6; trying Java 5 next.

Ok, it's definitely not setting executable under Java 5. Java 5 provides no mechanisms for chmod and friends, so we have been spawning the external "chmod" command. My guess is that this is failing to launch correctly, but either way this is a very problematic area for us. The same problem would exist under JRuby trunk/1.1, but we have also introduced JNA to call the real POSIX chmod function when possible, so it will happen much less frequently. I will investigate whether chmod is not spawning correctly under Java 5. Other suggestion are welcome.

Ok, it looks like an issue where we need to pass the absolute path when launching chmod; modifying it to pass the absolute path appears to make chmod work correctly. I will commit this to trunk and 1.0 branch.

Fixed in 4317 on 1 .0 branch and 4318 on trunk.