I maintain a module (http://drupal.org/project/csm) that uses a theme function to change the status messages that D7 displays in certain contexts.

The module works fine except when the Omega theme is used. When Omega is running, it also uses a theme function to change Drupal's status messages, and the function that my module defines is not run.

What determines the hierarchy for theme functions in Drupal 7? i.e., why is it that Omega's theme function runs, rather than the theme function defined by my module? Is there any way to change this hierarchy?