There is a deleted scene from Dog With Two Bones that shows Grayza taking command away from Scorpius and giving it to Braca. The previouslies come from that deleted scene. Weird, yeah.
The first half of season 4 is pretty crazy, and it took me three times to really get what was going on. So don't fret. Things will make more sense as the season continues.
aha! thank you. things are starting to make more sense the further i get into season 4... though it is still a bit crazy. i'll post some season 3 thoughts when i get home from work