Well I'l take back some of my comments in the following post. Through the miracle of the internet, and Google book search, I found some more information on why you heat milk before making yogurt.
The above table is from "Manufacturing Yogurt andFermented Milks" by Ramesh C. Chandan via Google book search. Chandan tells of the different manufacturing techniques for milk products. The reason for heating yogurt above killing the bad bacteria is the denaturization of the Whey Milk Proteins. You want to get around 85-90% denatured for the best holding of the water. You don't want to totally denature the protein, therefore, it is a bit tricky nature.
The table isn't perfect from my application since I heat up the milk in a double boiler, and the milk will be denatured as it raises through the various temp bands, but from what I can see, I should be allow the milk to sit around 15 minutes at 90C. I normally don't hold it at this temp that long (or at least I don't think I do, so I'll need to try and estimate next time I make yogurt).
You may want to try different hold times and see if you get better or worse yogurt.
Another interesting thing about the book is that the optimum range of temperature for growing the bacteria is 42-43 centigrade (109 degrees Fahrenheit) at 4-6 hours.