This article elaborates few nuances of using Runtime.exec() and Process. It will be helpful if you are working with Process. In fact the article gives code for running a dir command and reading its output.
Are you draining the error stream of the process? It may be that you are getting an error and hence nothing on the process' InputStream.
Also, is it possible to run a script that has all the commands that you need to run, rather than running one command at a time.