Maybe it's separation anxiety and she's screaming in anticipation of your leaving.
Perhaps just taking a little more time for cuddles or holding her hand, or something like that...? I'm not sure. We have to lie down with DS for him to go to sleep, but I'm not sure how that works when they're in a cot.
Only other thought is that maybe she doesn' like the cot. But that doesn't explain why it's ok during the day.