I'm sorry I'm not replying with a solution to your problem, but I'm curious what you came up with.
We have a predominately FCP environment already on Xsan, but we also have a Media 100. We were considering upgrading our OS 9 M100 to OS X and putting it on Xsan as well, but it sounds like that has problems.
I understand exactly the problem you're describing with the affinities and storage pools.
How many M100s are you trying to network? Do you also use the Xsan with FCP?