HTML tags are stripped off from emails
My Drupal setup relies on some other modules, but otherwise I have the same set up. I am not an expert (critics, take note!), but have you tried creating a new input format which ONLY contains the emogrifier filter?
I have all my standard filters in one input format that gets applied to all content types, and then I have a seperate input format which applies emogrifier as the post-filtering process in HTML Mail.
Just a suggestion. Daniel.