Well first of all please don't post links back to the software you're working on. There is really no need to identify it and some people might be offended by the idea that their code is under scrutiny. I edited out the link you provided and we'll leave it at that.
I nevertheless had a quick look at the application and confirmed that the file is protected by a new and little-known protection system. Which one is obvious if you know where to look and it is because of this that I'm going to suggest that you do not waste any more time on this. I'm afraid the protection used here is much too complicated for you to deal with, being at the stage you are.
Instead, I'm going to suggest that you learn about the Portable Executable (PE) format while you also read up on debugging and anti-debugging. Grab the PE specification from MSDN and be sure to check out Matt Pietrek's MSDN Magazine columns from early 2002.