It would seem that you can't set the WhatId (which you have) when the target object Id is a UserId. You can set it when the target is a contact or such. This post i found seems to confirm that hunch http://stackoverflow.com/questions/11105086/setwhatid-in-salesforce-using-email-templatehttps://stackoverflow.com/questions/11105086/setwhatid-in-salesforce-using-email-template