thind,
Likely you missed my comment on this question in the CB because you were busy writing this post. It is unfortunate because, from my perspective, you have repeated the same problem here - lack of clarity.

If you could forget for a second you know what your code looks like and what it was supposed to do and put yourself in our shoes, could you read your own question and honestly have the first clue what you were talking about?

Why don't you start out with the basics. Explain what the project is supposed to do, provide code examples showing it working (apparently without CGI::Application) and not working (apparently with CGI::Application). We will try and help once you have provided the clarity, detail, and code required to answer your question.