Things sped up after a few minutes. I don't know why it took a while. I did clear the cache and refresh the page.
Woops. I should have looked at the front end instead of Pingdom. The darn thing broke my theme and the front end looked deranged. Disabling it fixed things and put them back to normal.
I'm using Twenty Twelve for one installation and Twenty Thirteen for two others. All three were broken.
It didn't help to deactivate Better WP Minify.