Rails reading from wrong assets folder

Hi,
I'm having some trouble with the rails on my webhost. Something went
wrong when switching from 3.0 to 3.1 and configuring the assets
pipeline. Been following the guide:
http://guides.rubyonrails.org/asset_pipeline.html#upgrading-from-old-versions-of-rails

But it didn't do the trick. The weird thing is that I now have 2 assets
folders (I guess one got generates from rails or something) one in
public/assets and one in app/assets/, but it reads everything from
public/assets.

I'm wondering how to redirect the assets pipe to app/assets.

P.S The css and images works in this public/assets, but not the JS.