Found the answer. I had not ran the Domain Mapping plugin before switching it to a custom domain. So the correct steps should look like this:
- Create new site as a sub-domain (site.example.com)
- Point sub-domain at root (example.com)
- Point custom domain (site.com) at root (example.com)
- Visit admin page for sub-domain (site.example.com)
- Add custom domain (site.com) to Domain Mapping plugin
- Visit custom domain (site.com)
I had forgotten step 5 and tried to just edit the site to be at the custom domain instead of the sub-domain.
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