To add another possibility, ensure the user running Mango has permissions to read the keystore file at the operating system level. Logs would make it less of a guessing game, though.
Welll not long after I had placed the post I had discovered that I was missing the env.properties file under classes. So I copied it over from the working web installation and things began to happen as expected. That was a couple of weeks lost trying to figure it out and it is my fault that I did not ask the question earlier. I did learn that checking the "choose the createconfigfiles target" checkbox also fixed the problem so many thanks for your reply. Life is good now. :D