Aperture pictures won't show up in finder/itunes

I was recently having some weird issues with my OS. So I backed up all my files, did a clean install, and manually moved everything back into place. Everything seemed to be working great. I didn't realize it until today when I tried to put some pictures on my new iPad, but I cannot access my pictures in iTunes to put on my iPad or through finder (photos) to upload to something like facebook.
When I try to upload pictures to my iPad it says:
your aperture library could not be found. Open the preference window in Aperture and enable the preference to share previews with other applications.
Went and checked the preferences in aperture and it shows always allow.
When I go to upload a picture to facebook or Flickr I choose photos and the only option is iPhoto, no aperture.
Any suggestions?

Think I spoke too soon. I just synced 7000 photos with my Apple TV and thought everything was good to go. Now I just took some more pictures and imported them into Aperture and now iTunes says my Aperture Library has 0 photos! I repeated this routine of switching to an empty library and back, but it doesn't work any more!!! Help!

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