After 10.9 upgrade, settings keep getting deleted
So I found that after looking at the extended attributes that somehow this particularly problematic system had issues where there were a number of user immutable files.  After resetting the extended attributes things started to become a bit more sane.

For example, I found a handy command line option on the Apple forums:

find ~ $TMPDIR.. \( -flags +sappnd,schg,uappnd,uchg -o ! -user $UID -o ! -perm -600 -o -acl \) 2&gt; /dev/null | wc -l


(Drop off the final | wc -l to see actual files with issues.)

I then went through resetting things judiciously and selectively executing these where appropriate (also found on the Apple forum, but modified from original form):

sudo chflags -R nouchg,nouappnd ~ $TMPDIR..
sudo chown -R $UID:staff ~
sudo chmod -R u+rwX ~ 
chmod -R -N ~ # Or specific paths


For example, I found that even after executing these and rerunning the find command sans the postfixed line count that there were still a number of corrupt permissions and had to selectively run chmod -R -N on those paths again.  Odd that it didn't take care of them the first time, but ultimately I ended up with a 0 count of permission afflicted files.

For good measure I took the advise of rebooting into the recovery partition and running Terminal -> resetpassword and subsequently reset the folder permissions for the homes, but I don't think that that was necessary as the permissions seemed to checkout prior to that for the folder and children.