Anyone have Custom Domains and Clean URL's working together?

I'm wondering if anyone has found the .htaccess magic to get both Clean URLs and Custom Domains working together.

In the control panel for my test prof (openscholar.dept.u.edu/testing/?q=professor/cp/settings/generic) I can put in a custom private domain, professor.dept.u.edu. I tell apache that professor.dept.u.edu has the same doc-root as openscholar and viola! professor.dept.u.edu takes me to professor's openscholar page.

If I turn on clean URLs in openscholar professor.dept.u.edu gives an Internal Server Error, 500.

On the other hand if I remove the custom domain, clean URLs work fine.

So far I have a pretty standard .htaccess

RewriteBase /testing
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !=/favicon.ico
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]