Yes, I had the same problem earlier (see the thread on required 'ox-publish). Here's what I did:
First, I noticed that the packages get loaded only after initialization, so I put my org-related initialization script in the after-init-hook. Then after other people here told me about (package-initialize), I just placed it somewhere in the beginning of my emacs initialization script, and it worked as well.
I also removed a similar script for setting up babel since I noticed my installation works without it anyway. I think those languages are supported by default.