Aperture 3.3.1 Import fails on hard drives, but not SD cards (bug??)

After countless hours of research and attempting the A3: Troubleshooting Basics (http://support.apple.com/kb/HT3805), I have found a weird bug that I can reproduce.

If you import images, the import window will show some folders on a hard drive (and the corresponding images inside them) and not others. These exact images are viewable on an SD card. When clicking on a folder, it says "Loading Assets" for a second and then shows nothing. It doesn't matter what brand of camera, when the photos are taken, which hard drive. (Import is set to not exclude anything either).

I have tried the entire Troubleshooting Basics guide (creating a new library, using the first aid tools, deleting preferences, even a fresh install A3). I even tried different hard drives (all Mac formatted and have worked with Aperture before). Lastly, I even tried my other Macs with fresh copies of A3.3.1.

The final test was rolling back. I deleted all the old Aperture files (app, plists, etc...) and loaded Aperture 3.1 Trial that I had laying around. Surprisingly, it found the images as normal. However, once the AppStore updated to 3.1.1.... same behavior.

Any suggestions?