FIXED!

I dug around a little bit more and here's how I fixed the problem, not sure if only one step or all of them together so I'm going to list everything I did!

1. Go to help in Eclipse and Update Software (Update everything you can!).
2.Download latest LibGdx setup file (last one was out few days ago)
3. Rebuild the project you want to make
4. IF you run the desktop or android app the first time, it's gonna fail (on PC and your android phone both)
5. Go to Run->Run Configurations->Desktop Launcher->Arguments tab. Then click other in the working directory tab and choose Android/assets folder as the default working directory
6. Run your apps and the app should be working fine on both platforms (it is for me)