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Thanks for your inquiry, and sorry about the silence. I have two nearly full time jobs and can't always monitor AppleJack as well as I would like.

1) Just so I know exactly what you mean, what is "phase three"?

2) Assuming "phase three" means the third option (cleanup of cache files), I will also assume that the first two tasks went fine: (disk repair and permissions repair). Can you confirm that? (Look at /var/log/AppleJack.log)

3) What kind of computer experienced this issue? It looks like an Intel Mac issue.

4) Can you tell me if there are any custom extensions, or any modifications made to /etc/rc that I should know about?