Ah, indexing seems to be another issue I just noticed. The new shows I download do not appear on my BD player until I run a re-index in media center. But I think that may be more of a 4.1 beta issue than sb.
Also, no checkbox for the season folders. Just the box to specify formatting.
Still, I can't really complain if all I have to do is move episodes into season folders. Still beats the hell out of doing everything manually like I did before my Syno.