I can't seem to find a logical reason why this is happening, as all season folders for Simpsons are identical in naming convention.
My naming convention is this:
TV Shows/[ShowName]/Season [N]/[ShowName] - [Season&Episode] - [Title]
The following seasons DO appear: 1,2,3,4,5,6,7,8,9,13,17,18
The following seasons DO NOT appear: 10,11,12,14,15,16,19,20
TV Shows/Simpsons/Season 1/Simpsons - 101 - Simpsons Roasting on an Open Fire.avi
TV Shows/Simpsons/Season 10/Simpsons - 1001 - Lard of the Dance.avi
TV Shows/Simpsons/Season 16/Simpsons - 1606 - Midnight Rx.avi
Any ideas? If you need additional info to reproduce, let me know.
[Edit: Boxee has been up/running for 3 days on my MBP]