Aperture has a bad memory and has gone confused

Aperture 3.0.3 has a bad memory and has gone confused... or is it just me?
I have several referenced files that are quite confusing.
This is what I see in list view:
Version name: filename
Filename: filename.cr2 (Canon raw file)
Camera model: iPhone (doesn't shoot Canon raw)
The same file in Locate referenced Files-dialogue:
Version name: anotherfilename
Filename: anotherfilename.jpg (not Canon raw anymore)
Both views show the same date. The image is shot with my Canon.
Are you confused? I am.
The bad memory is frustrating. Almost every time I start Aperture I also had to reenter my preferences (thumbnail size, external editor etc). This is discussed in http://discussions.apple.com/thread.jspa?threadID=2565307&tstart=0.
I have some tother issues too. Aperture doesn't help me anymore. It prevents me from doing what I love - making pictures.
I have rebuilt and repaired the library.
I have followed Troubleshooting Basics http://support.apple.com/kb/HT3805.
I'm out of ideas and would really appreciate if you can help me.
Thanks!

Thanks!
No, I'm no importing RAW+jpg and I haven't been editing metadata manually in the library. I don't even know how I would do that. Any suggestions about which appliccation it could be? Photoshop? Painter? Mail?
I have other issues too and that makes me think that there had to be something else too. Face detection is running wen it's turned off and number of versions doesn't show when the settings is set to Show number of versions.

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