5.3 project says it is 5.0 when importing repository on different computer, breaks project

I set up a 5.3.5p8 project on one computer and then made a bitbucket repository and then imported that repository on a different computer. When I start up the project, it says the project is was made on 5.0 and needs a re-import. When I re-import, all my object images, positions. scales etc are all off or missing. It's a similar issue to this thread:

http://forum.unity3d.com/threads/your-project-was-last-opened-with-a-different-setup-of-unity-after-delete-library.392356/

I didn't commit the library folder, but I did include Project Settings. Is there a way to fix this, do I have to commit the library folder?