We have written a custom code behind for a SP2010 master page. The class is
compiled into a dll, packaged into a wsp farm solution, and deployed into the
GAC. The master page is configured to inherit from the custom code behind using
an assembly directive.

We have 2 site collections in the same web application. In one of the site
collections, the custom code behind runs fine for all users. In the other site
collection, the custom code behind runs fine for everyone except anonymous
users. I'm having trouble figuring out why.

Here's some more information:
Both site collections have identical copies of the same master page.
Both master page files are fully published and approved.
Both site collections are configured for anonymous users to have access to the
entire site