So to recap; Aperture cannot see any files or folders in the home Pictures folder. Even if you make a new user, log in as that user, run Aperture, Apertute does not see anything in that users home Picture folder.
Is all that correct so far?
In addition you say you are running a plain OS X install the Home and Picture folders on on the root drive and nothing has been done to them. (why that ACL is set on your Picture folder should be investigated at some point).
Getting the complete ls output for the Pictures folder, as I showed, would be helpful. Also a screen shot of Aperture's input window could be helpful.
I'm running 3.4.5 on 10.8.4 with no problems as are most folk here so this isn't strictly an Aperture problem but some weird interaction on your system. When did you upgrade to 10.8.4?
Also can you access the Pictures folder with other applications? Finder, iPhoto, Preview, TextEdit, etc.
Thank you everyone for your help..
Spent a few hours with a number of Apple "Genius'" folks. All of your suggestions covered exactly what the Geniueses suggested to do. Turned out to be the stumper of the day for them. Fortunately, the fault was found.
Turns out that one single AVCHD video filein the target folder had a format that was incompatible with Aperture. It's presence made the entire folder's content of 5000 photos invisible.
Regards to all