Alright, so I decided to rewrite the application from scratch.
I kept the basic GUI design, with only a few minor tweaks here and there. There are numerous tweaks done to the underlying system, but nothing that really effects the ender user too much. I did add a few little details, such as double-clicking to edit commands, a better copy/paste function, mouse tracking when using capture mode, and a couple more, but it is pretty much the same at this point. And now that I have the source code back, I am also releasing that if anyone should like to learn anything from it.
The hosting has also been moved from Dropbox to SourceForge, as will likely any future project I create. No more losing entire projects for me.
One last note, I changed the targeted framework from .NET 2.0 to .NET 4.0. This shouldn't effect most people, but the link to the proper framework is given above if you don't already have it installed.