Linc
Appologies for joining the party uninvited, but I too have exactly the same problem (although I've never heard of Alfred) - opening a link from Apple Mail, or just opening Chrome and AGAIN being asked if I want to set it as my default browser is how I know the "this solved my question" answer doesn't (on it's own) work for me.
I also get a huge list when I try your:
find . $TMPDIR.. \( -flags +sappnd,schg,uappnd,uchg -o ! -user $UID -o ! -perm -600 -o -acl \) -exec ls -Odel {} \;
When I try your sudo I get:
Martin$ sudo chflags -R nouchg,nouappnd ~ $TMPDIR.. ; sudo chown -R $UID:20 ~ $_ ; chmod -R -N ~ $_ 2> /dev/null
sudo: can't open /private/etc/sudoers: Permission denied
sudo: no valid sudoers sources found, quitting
sudo: can't open /private/etc/sudoers: Permission denied
sudo: no valid sudoers sources found, quitting
I do have a login password and am not asked to enter it (as you can see above).
I am also wondering what would cause the mass change of permissions, and whether it's also behind the significant number of application crashes and shut down failures I get each day (and if it's also responsible for lost socks and all other ills?)?
I am running OSX 10.8.2 following a clean install of 10.8 on a Macbook Air 1.8 Ghz Core i7 with Safari 6.0.2 and trying to set Chrome 23.0.1271.101 as my default browser.