I know this thread is years old, but I experienced the same problems with Sametime 8.
The reason for this is indeed the INI entry DominoCompleteDoctype set to 1 or 2. In my case I really forgot that I even had that value set, but it came from a server configuration in the NAB valid for all servers.
The solution is to set the INI value to 0 on the Sametime server. Here is some info from IBM on it: http://www-01.ibm.com/support/docview.wss?uid=swg21308399
Edit: forgot to actually paste the link