Yes, I used to have to do all these things, but with the current version of snow leopard and FCS3 you no longer need to cheat to get it to read them in the right order.
Hmm...I'm on FCS2 w/ Leopard and Encore CS3 for Blu-Ray. Dang, I've got to upgrade all three! If FCS3 could burn BR it would be worth it, but no. /rant
Do you recall which fixed the problem, FCS3 or Snow Leopard?
Sorry I cant, I installed everything at the same time on my older mac pro and new one didnt check before i dropped fcs3 on. But I would suggest its do with Snow Leopard.