2.1 wp_notify_postauthor override

Recently, I wrote a plugin that overrode the core wp_notify_postauthor function to change the email format to HTML. It worked beautifully until I upgraded to 2.1.

Now, even though I have deactivated and activated the plugin several times, the plugin is getting ignored completely and the core function fires. It got ignored for the first few comments, then I deactivated and activated, and it worked for a grand total of ONE comment.

The next six comments were all the core function again.

Any idea why this function is suddenly not getting plugged randomly in 2.1??