Raw Folders not appearing after update

I just updated to the new version today and after I did when I start a new project it won't create a new folder for it in finder.
To explain further, I have my Aperture library in a folder on my HD called Aperture Files. This also houses a folder for every project I have created in Aperture and in those folders are the pics from those projects.
When I would import a pic before the update it would send the file to the Aperture Library and put it in the right project folder. I have created 3 projects and none have folders for them now.
I goofed today when I tried to delete a version and wound up deleting all the masters from that project. I had to reimport them. Not that big a deal as it was a small project that I had done little work on. Could this have messed things up?
What's the deal? Can I fix this easily?
Any help would be appreciated.

Correct me if I am wrong, or tell me that I am correct, but I think that I just realized that I really have no need for there to be folders outside of the Aperture Library for my raw pics. If I need them in a folder as raw I can just export them as such.
It makes more sense to have Aperture's Library handle all that so that they are all in one location and I am not having to searh for them over 4 different hard drives.
After looking at some of the tutorials I came to this conclusion.
Tell me if I am on the right track.

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