Because I’m using WP Super Cache to reduce the strain on the server, there’ll be a lot of older posts and pages with the old theme. I didn’t notice this until I loaded up my blog at work. The main page was fine as it’s incredibly dynamic, but many of the pages (as opposed to posts) were stuck with the old theme.
I also noticed it’s often stalling before it can finish, so I changed it from every 12 hours to ever 24 hours. If that works well, then at most a few days from now everything will be on the new theme.