Alright folks! Figured it out!
Turns out it has everything to do with Eclipse's updates, in which in generates the activity a different way than it used to. Instead of generating it with just the layout it also has the fragment layout thing which I still have no idea what it does. Using another users question, I did what other user's told me and got rid of the fragment file and made minor changes on the activity class file.
This worked like a charm yesterday, or so I thought... Until today I decided to change some things and they wouldn't change anymore. The error was in the menu files which are also generated, I just had to delete a couple of lines which made no more sense now. That was it!
Uhh... Now just to get something off my chest: I HATE HATE HATE HATE this update so far it has given me nothing but problems!
Thanks for all your help everyone!