None of my config or startup files have any mention of "--skip-show-databases". I didn't even know there was such an option.

Is there somewhere I should look other than /etc/my.cnf, /usr/local/etc/my.cnf and /etc/rc.d/rc.mysql if mysqld is being started by root. According to find -exec grep, the phrase "skip-show-databases" does not appear anywhere in /etc.

The permissions look right to me. What permissions on what files could cause "show" to fail while "select" works normally?

mysqld was indeed running as root, although I specified user=data when I configured it and set user=data in the startup script that was running it. I prefer to have one user for all of my database daemons as opposed to user msql for mSQL and user mysql for MySQL and user pgsql for PostgreSQL.

I manually restarted it with safe_mysqld --user=data and encountered even more problems, because "data" didn't own /usr/local/var. I changed the data directory to /usr/local/var/mysql, and chown'ed that to "data", because /usr/local/var is used by other programs, including Gnome.

Now mysqld is running as "data" and using /usr/local/var/mysql as its data directory. /usr/local/var/mysql and all of its subdirectories, and all of their contents are owned by "data". /usr/local/var/mysql is mode 755, subdirs are mode 700, and their contents are mode 600. After all these changes, I'm still having the same problem. If those are not the correct permissions, what are?