Thumbnails are often the wrong orientation and distorted. What is causing this?

Thumbnails are often the wrong orientation and distorted. When I select in viewer they are normal again.

As if only the corrected layer would have remained on the photos.
So the geometry of the pictures is correct - they are not skewed or something? Only the colors and intensities are wrong?
. Only in printing when it is converted to PDF file some photos are unrecognizable.
Is it the printed pdf or the pdf viewed on the screen? If it is the printed copy you need to fix your print settings.
Does Aperture give a warning, that the high resolution images are not available?
We had some cases of books not being able to be printed, and that was due to a broken reference to the original files. Only the book could not access the originals, all other parts of Aperture could. To check for this, try to add one more adjustment to one of the images in question. Is it possible? Are the edits reflected correctly in the pdf of the book?
We were shooting with 3 cameras, Lumix5 shooting RAW, Cannon 100 shooting JPEG and SONY alfa850 shooting RAW.
Have you tried to reprocess the raw of the edited images? (Photos > Reprocess Raw)
Also try, to remove one of the images from the book and to add it again. That usually helps, if Aperture has lost the connection to the originals used in the book.
If you no have done so already, repair (and if necessary rebuild) the Aperture library.
See: Repairing and Rebuilding Your Aperture Library: Aperture 3 User Manual
Regards
Léonie

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    10/22/13 9:41:59.000 AM kernel[0]: CoreStorage: fsck_cs has finished for group "3FD474FF-B711-4557-9B01-67EB19C49BDA" with status 0x00
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    10/22/13 9:41:59.000 AM kernel[0]: USBMSC Identifier (non-unique): 10000E000C7F9033 0x59f 0x621 0x0, 2
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    10/22/13 9:41:59.000 AM kernel[0]: BCM5701Enet: Ethernet address a8:20:66:0d:fc:25
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    10/22/13 9:42:06.598 AM airportd[74]: _processDLILEvent: en1 attached (down)
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    10/22/13 9:42:06.682 AM mDNSResponder[50]: mDNSResponder mDNSResponder-379.38.1 (Apr 25 2013 19:19:56) starting OSXVers 12
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