You might consider this a bug, but after having been bit by it multiple times, I figured it would be best to post it here.

When you have multiple apps on a server and you re-arrange the primary domains on them, changing which app a specific app uses, the server will not properly follow your new primary domain settings and will instead load your default app. Here is how you reproduce the issue:

1. Have an app on the server with a domain like dev.mysite.com
2. Have a second app (your production app) on the server with a domain like mysite.com.
3. You want to launch your newly developed site, so change the primary domain on your production app (mysite.com) to old.mysite.com
4. Change the primary domain on your first app (dev.mysite.com) to mysite.com
5. Visit your site. The app you want won't be the one that loads, instead, it will be the server default app. For some reason, the server gets confused when you rearrange primary domains and begins to ignore the settings. Restarting, purging caches, etc. does not resolve the issue, only a ticket to support or a modification of your server's default app will resolve the problem.