jwrapper manipulates application jars somehow, and is resulting in a non-functioning jar: at runtime it throws a "MyClass cannot be cast to MyClass" type error. I believe this is caused by re-evaluating code that creates a class loader, leading to multiple instances of class MyClass being loaded.
The jwrapper docs don't describe the changes made to the jar, except for the use of pack200. I've tested pack200 in isolation, and it does not cause this problem.
I've also tested the jar built by jwrapper without using the wrapper executable, by passing it to "java -jar". So it's not jvm transmuting, or anything else that the wrapper is doing: the jar itself is broken.
UPDATE:
jwrapper allows skipping pack200, but then the install file is huge. Since pack200 works when run standalone, I could work around this if there were some way to tell jwrapper that the file is already packed. Using <Pack200Exceptions> doesn't help, because then it doesn't know the file is packed.