One: For example, Apple may have a patent that it feels is not part of the consortium's IP. If Microsoft starts to infringe on the Apple patent, and then claim it's part of the Novell package - so fair use - they will need a way to sort that out. Possibly the consortium's admin section includes a mediation function, and the partners have agreed to be bound by it's decisions. This would be a lot cheaper than settling things in Court.
Two things:
1) ownership of a given patent won't be in dispute. They are like property. They initially belong to the inventor. The inventor may assign (i.e. sell) the patent to anyone else, who then may sell it again, etc. Usually these sales are recorded in the USPTO. In any event, if someone claims to own the patent, he will have a document that shows that he bought it.
2) patents do not give you the right to do anything. They only give you the right to prevent others from doing something.
So if MS starts to infringe an Apple patent, it can't defend itself by saying that it is actually using the Novell patent. (It may be true that the product uses both patents, in fact, but the fact that MS "owns" the Novell patent doesn't give it the right to infringe the Apple patent).