Yes, the cwd is that of the java program, of course. The linked document (if I remember right) covers this point. If the batch script depends on cwd, then you are going to have to change the batch script or write another batch that does a cd then calls the batch script you actually wanted to call.
The other option is to read the API docs and pay attention to the ProcessBuilder class (and its directory method), as Runtime.getRuntime().exec() should not be done directly anymore. You have finer and fuller control using ProcessBuilder.