Sometimes the thread execution process time is higher than JVM thread waiting process time, it use to happen when the process you're invoking takes some time to be processed, use the waitFor() command as follows:
try{
Process p = Runtime.getRuntime().exec("file location here, don't forget using / instead of \\ to make it interoperable");
p.waitFor();
}catch( IOException ex ){
//Validate the case the file can't be accesed (not enought permissions)
}catch( InterruptedException ex ){
//Validate the case the process is being stopped by some external situation
}
This way the JVM will stop until the process you're invoking is done before it continue with the thread execution stack.