Looking at the error in the console window, do you have 'gba.dll' in the local folder? If so, do you have any other gba.dll's in your path environmnet? Which version did you download? It looks like you got the version 0.2 because I can see that you have the command-line "RegisterProject" program, which is an old version. Actually, did you mix-and-match versions of the download? Don't do that.
Sorry, but VB.NET is absolutely one-hundred-percent disgusting in every way I can imagine. A few less kilobytes in program size ( in my opinion ) does not warrant using a horrid language that needs to vanish ( along with java ).
I've noticed the large file-size myself. The jump occurs when the GUI program is added, I'm not really sure what's up with that. I may just need to pass some optimization configuration options in the release build, but who knows. It might be the icon I included, which has all common sizes up until 512x512 and has alpha transparency. That actually probably is it, now that I think about it.
I saw your program, and tbh I have absolutely no clue how it's pertinent to GBA hacking, just that it's a general-purpose versioning software that uses a bindiff method. While our programs do share the versioning concept ( albeit, that's all that mine does right now ) the overall purpose of my program is a bit larger. Also, 401kb isn't exactly large. It still takes < a minute to download, which is really the only time you really should worry about file-sizes.
I actually agree in that VB.NET is disgusting... But as I always say, you have to put up with it for the sake of beginners. I'd much rather just do everything in C++. You are probably the same.
When I checked the unzipped filesize, it was almost 10 MB, so that's what I was concerned about. People today want minimalist software for seemingly small tasks.