Sorry for all the questions today :), but I've been flying a lot today and had a few questions pop up. When flying I notice a difference between the reported wind in fs9, using the "shift+z", and the FMC that says "actual wind". On my last flight the fs9 reported wind was 88/19 and the FMC said 106/19. I suspect it might be something like one is magnetic heading and the other is true heading.

Your suspicion is correct. Though I don't remember which shows which. The wind reported on the PROG page should be the same as FS reported winds.Cheers,