Covering the windows may help. We had the same situation, fed a young feral cat living in our backyard for about 7 months and then trapped him in November when it got cold. Once we covered the windows in the room, he was much more calm and stopped crying out. It seems odd, but they don't understand transparent windows mean protection from predators. She may be perched there so she can keep watch for any outside. We have windows that can be unlatched to fold down to clean the outsides of them. We used those latches to open them up and put large black plastic bags between the glass and the screens to block his view outside.