Hi David, and welcome to the Ranch!
I'm only guessing now, since you didn't provide the source code. Common mistake when running external processes from Java is the failure to consume standard output and error stream of the external process. Your issue might belong to the same class. Please read
this (somewhat lenghty) article, it should help you to execute an external program flawlessly.
If this does not help, post the relevant code here. We'll try to have a look at it.