Hi R.,
I think your 4 year old daughter needs to have her own room and not bunk with a 6 year old boy. The 2 year old could share the room with the 6 year old since they are both boys. Also it sounds like she might be having some nightmares. Or the 6 year old boy may be taunting her and pretending he's sleeping when you and your partner goes in to check on her. Also, what exactly is the routine for your daughter right before bedtime? Something is going on in that room at night. May be you can hide a video camera and tape for a few days to see what is going on before she falls asleep, or doesn't for that matter, or why she wakes up so suddenly crying during the first few hours of bedtime. I hope you find out what's wrong and soon. Best wishes, and God Bless! G.