I have been having ongoing issues with my rennet setting sometimes and not others.
Today I got a batch of milk straight from the local organic dairy. Heated and then cooled a pot of it, and it would not set with more than the recommended rennet.
Grabbed a sample of the same milk - still raw - and heated it and added rennet, and it set within minutes.
Tried twice more with pasteurised milk that I had put in glass jars and heated to sterilise, once in a different pot, and once in a glass cup. No luck either time.
tried once more with a small sample of raw milk - luck within minutes again.
I'm not a cheese maker, but a chemist, so I'll speculate as a chemist...
If milk has been boiled the protein structure changes and it may not coagulate. The change also occurs if the milk is held over about 150 F for any length of time, and it occurs rapidly at near boiling temperatures. A very common pasteurization method for milk is 145 F for 30 minutes.
Biological chemical reactions are highly sensitive to temperature... A good rule of thumb is that for every 18 F increase in temperature the rate of reaction doubles. Rennet works slowly at temperatures below 86 F. Optimal reaction temperature is about 108 F. Rennet is destroyed by temperatures in the range of 120 to 140 F.
So my recommendation would be to use an accurate thermometer to measure the temperature of the milk. If you pasteurize do not let the milk get over 150 F, and especially not to boiling. And only add rennet when the temperature is perfect for it's action. There may be slight variations in temperature recommended by different rennet makers, so follow the temperature and dose guidelines on the package.
Sadly, the regulations on pasteurization set the minimum temperature, but not a maximum. If your dairy pasteurized that batch at >160 degrees, it has done just what Joseph said and can't be undone. We have about 50% failure rate with commercial milk, organic, local, big box, there is no pattern, not consistent among brand either. The only thing that is reliable is raw milk. When making a soft, non-aging cheese, we just do the low temp pasteurization first if we are worried about it. Usually not, but if I'm serving it to my 91 year old WWII vet friend or small children, I'm not taking chances.