A client, who uses your plugin, has asked me to look into some disappearing posts in their Author archives. (At least the full year of 2012 is missing from the list.) I've confirmed that the posts returned by wp_query is also missing the posts is question, and through some experimentation with the query have identified the "HAVING MAX( [...] ) <> 1" clause as the problem. (At least, I've discovered that when I delete this clause from the query, we're getting all the missing posts).
I believe this clause is added by the "posts_groupby_filter" function on line 585 of the plugin's main page, but figured it would be worth running by you before I spent too much time reverse engineering your plugin.
Have you come across this issue before? Do you have any recommendations for how I can restore the archives, and prevent this from happening again? Any help would be appreciated. :) Thanks!