Raw milk yogurt is much trickier to make than pasteurized. When I first started making it, some batches were really wonderful and some did not turn out at all. To make matters worse, many of my problems were clearly seasonal, so it took me a couple of years to understand everything well enough to consistently produce great results.
The biggest thing I have learned is that 90% of producing great yogurt is using great milk. Here are some common problems and what I have learned about them:
The yogurt never actually "yogs":
1) There is too little protein in the milk. The gel structure of the yogurt is due to cross-linking of the proteins. It can be difficult to make yogurt during the first two months of lactation when the milk is naturally low in protein. July and August can also be difficult because there are few pasture plants with high protein during this time.
2) The cows are eating a lot of plants that are high in sulfur. Legumes (alfalfa, clover), Canada thistle, kochia, and lambsquarter are naturally high in sulfur and occasionally grasses are too. The sulfur compounds in these plants are readily oxidized into thiocyanates which are strongly antimicrobial and thus inhibit bacterial growth in the yogurt.
3) The cows have mastits. High somatic cell counts (SCC) cause the protein concentration to be low, displaced by sodium and chloride ions. With little protein, there is nothing to cross-link and create a gel structure.
The whey is separating out:
1) The milk has low milk solids, especially protein.
2) Too high of an incubation temperature was used (in which case, it's no longer raw!)
3) The yogurt is getting older. The protein bonds relax over time and allow whey to leak out.
4) The yogurt was cooled too soon after it "yog'd". Yogurt often "yogs" at 8-10 hours, but if you leave it a couple of hours longer, the gel network becomes more stable and there is only a slight increase in sourness.
The yogurt doesn't taste very good:
1) Very sour - Too much starter culture was used so the bacteria doesn't have room to grow.
2) Bitter - This can be many things: The type of starter culture, the age of yogurt (bitterness develops over time), mastitic milk, or strongly flavored weeds in the diet.
3) Clabbered milk flavor - The milk was too cool when the starter culture was added, so natural milk bacteria grew more than the yogurt specific ones. High bacteria counts in the milk could also produce this.
The cream is very hard:
This is actually a good problem, health-wise. Harder cream is higher in short-chain (more stable) fatty acids. Both the breed of cow and the individual cow can affect this. Also, long-chain fatty acids (less stable, but creamier) are higher in early lactation or if the cows are supplemented with oil seeds (cottonseed, sunflower, soybean).
Part of the milk yog'd, part didn't:
The culture was not thoroughly mixed in. If you are using actual yogurt as your culture (instead of a powdered culture), pre-mix it with a small amount of milk. Make sure there are no lumps before mixing it into the milk. Stir well.
There are hard, slightly yellow lumps in the yogurt:
If you are using cream-top yogurt for your culture, remove the cream first. It never fully incorporates into the next batch. Low-fat yogurt works best for the culture.
Hope this helps with your yogurt endeavors. There's nothing quite like the taste and silky texture of perfect raw milk yogurt!