Impossible to say without a deeper inspection of the system, but given `/dev/random` does block, the answer is something is redirecting urandom to random. On the system, does cat urandom ever block? Step one is the reproduce it outside of Java and if that's not possible, start digging into the Java library's code. If it is, then start digging into `glibc`, devfs, the kernel.

Something in the chain switched urandom and random. Isolate each component until the culprit is found.