Im sorry to here that you have problems, but i haven't the time to debug the problem. If you are a Programmer and found a solution, then it would be nice you contribute the solution.
I assume there is a problem when saving the files.
First: there shouldn't be "new" files. The plugin only overrides the existing ones (if you uploaded normally) - it uses the standard path for saving them (so make sure you don't do any fancy stuff with folderpathes).
You my have look an these comment i posted a few weeks ago about enhance the debug view: