Java Runtime.exec(COMMAND) doesnt work in win2K8 R2-Collection of common programming errors
You can run the program manually from the command line. You can run the program from within the parent process using the full path specification. I would say we can assume the program runs properly.
What else could be different? The environment the parent process is running under perhaps? I would check the PATH before launching the process. You are using Java. Too many Java programs use batch files to launch the JVM process. This batch file could be mucking with the PATH variable.
If this is your program and no batch file in involved I would check the current working directory when you run the parent program. It could affect what gets found at runtime as well.