The fat in homogenised milk often sticks to the proteins, giving you more fat in the final cheese. With the non-homogenised milk, you would end up with more fat in the whey. This would explain both the lower yield in the main cheese and the higher yield in the ricotta. I have been told that large scale stabilised paste bloomy rind cheeses are often made with homogenised milk because they get higher yield. Also, due to the way that the fat sticks to the protein with homogenised milk, it retains more whey. Having said that, I've done a fair amount of playing around with both homogenised and non-homogenised milk recently and I get pretty similar yields with both. The curds are *completely* different, though, so I'm not that surprised that you see a difference. You may just need to dial in your technique.
Also, as Bantams said, if you are getting milk from a small producer (possibly even from a single cow), you will get *much* higher variation in the milk than standardised milk from the supermarket. Normally standardised milk will have a higher protein to fat ratio, but it depends.