I had this same problem tonight and was pulling my hair out for a couple hours. I started commenting out my code and noticed that this starts happening after I use mysql_connect() in my functions.php file.
I read about mysql_connect() and apparently it always makes a new link to a db UNLESS the same user and pass word are used to connect!
I realized I had wordpress system and my custom save_post methods using the same user/pass combo and this was messing it up.
So created a new user for my custom save methods and it stopped happening.
Hope this helps!