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Everytime I restart/boot my mac and open up a mail application (thunderbird) or a web browser (firefox or chrome) I am always asked if I want to make it the default. This happens even if I click yes.

So, for some reason osx isn't remembering what I set as the default mail or web browser. I have already repaired disk permissions which didn't fix the problem.

Any ideas?

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The permissions was a very long shot for this issue - but do reboot into safe mode (or run a repair of the filesystem using fsck/Disk Utility) and report back. Another thing to try is to make a new user account and see if things stick there better. I'd guess a corrupt preference file is hosed, but you might have to be systematic about troubleshooting this to find the glitch on your mac ... – bmike Sep 15 '11 at 16:45
Definitely try that! – daviesgeek Sep 15 '11 at 17:22
Are you using FileVault, by chance? – kopischke Nov 5 '11 at 2:26

The problem was I was using the root user. Creating a new user sorted everything out!

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Try to set default apps with RCDefaultApp

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Tyr setting it within the Safari or Mail preferences as described here:

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