Referenced files do not show same folders as in iPhoto/Aperture

I built my Aperture library based on all the previous work I did in iPhoto. Piece of cake! Then I copied the whole iPhoto folder (including aperture files) to an external drive. Using the finder, it shows the proper file path to the images, but when I "manage referenced files" through Aperture, folders such as "originals" are missing so I cannot reconnect the library. It seems to be seeing only certain folders. What am I doing wrong?

Not sure if this in an intentional move by Apple to discourage from combining Aperture masters and iPhoto libraries. It is bloody annoying. I finally bit the bullet and have begun copying all my iPhoto masters into a separate folder structure just for Aperture's library. I will then remove many masters from the iPhoto libraries except family photos my wife needs to access.
I will then have to relink thousands of images by hand (already begun...). Another annoying "apparent bug" with Aperture is that is won't search and relink multiple images properly unless they are in the same folder. Final Cut Express, on the contrary, will search my entire directory structure to try to find the external video references. Not sure why Aperture is so crappy at this...
A lovely little by-product is that a number (estimated 15%) of my referenced images that I am trying to relink have become corrupted such that Aperture thinks the original file is something other than the file it was. (?) I have to delete the versions in this case and replace the versions with the correct images. I am afraid that I will lose all editing on those images, but haven't really tackled the problem yet. Some examples of these corrupted reference images are below:
http://www.flickr.com/photos/bradsteelsgallery/4396430491/sizes/l/

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