Ok, I figured out the problem.
This website: http://wiki.jumpbox.com/doc/runtime/faq/install_phpmyadmin

told me that I needed to do the following to fix the htpasswd.setup file:
sudo htpasswd /etc/phpmyadmin/htpasswd.setup admin

For whatever reason I could not find this in the documentation for
phpMyAdmin nor in any of the forums, howtos, etc. I searched.

I don't know if this is something that needs to or even should be solved
at the package level--you can mark it fixed if not, but someone should
really update the documentation somewhere to reflect that this is an
important step to use the configuration script for the package.

-- 
phpMyAdmin: can't authenticate to run setup.php script
https://bugs.launchpad.net/bugs/382824
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