Creating and running JARs from Java programs

OK, I have been googling and searching, but this is something I cannot work out, so I raelly need some help.
Basically, I am building a GUI app that would generate, compile and run java programs. And I also want to enable the users to create JARs they can later double-click if they want to run the program.
I am using Runtime to compile programs and it works just fine. When I click on a button to create a JAR, my application creates one, but when I double-click on it, it can't find main and it exits. Now that is not so much unusual, but I am positive that my manifest file is OK, because when I run the same command from the command line, then I can click on the JAR file to run it.
So what is the deal here? I mean, why would a JAR file created from the command line run and the one created through a GUI app using the very same command could not find main?
Any help would be graetly appreciated.

again, another unanswered question.
BTW I'l keep bumping these until I get an answer that works. I have been up 3 hours now trying to get this sorted and it's something that netbeans is supposed to do on its own!?!?!?!?!
Hello, SUN, is there anyone there???
No, didn't think so.

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