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Hi !
First of all, I am sorry to hear that you have had these issues !
Just to let you know, Disk Utility should be able to take care of all permissions issues on your volume that might have been created by an installer. Indeed, it checks a file left by the installer itself to do its work and, unless this file has been manually removed, will find the necessary information. Permissions that you or a faulty application have altered for an uncommon specific file or folder are another issue but, up until now, it always repaired them on my various test Macs.
The node issue seems to indicate that the problems you were having are more related to a low level hard drive glitch than a software problem. Just to let you know, Disk Utility should also have been able to take care of most catalog problems -- although you are right about the fact that some problems can require the use of specialized software. I have never run in to this myself, though.
Your description made me wonder wether you used a special disk utility or "un erase" application ? Incompatible ones are likely to create hard drive catalog issues similar to what you experienced.
Without having a look at the iBook, this is of course speculation on my part. However, even though issues can always happen with any operating system, as you point out in your very interesting blog, a software update is unlikely to cause such a "disaster" in itself... Something else seems to have been at work.
F.J.
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Would you think that the service you got at the store wasn't appropriate, you can call Apple Customer Relations and describe the issue. Your comments will be taken into account and forwarded to the appropriate team. Their number can be found on the "Contact us" pages on Apple.com.
The "Geniuses" are normally extremely knowledgeable although, of course, nobody can have universal knowledge.
F.J.