When a room is entered, the description prefix is supposed to display "You are in [room]" and "You can go [exits]." However, for some reason, this message does not appear on all my rooms, only on some. Why is it doing this and how can I fix it?

This is a "problem" in Q5.2. If you use roomdescriptions with a script, it only displays the text generated by the script. This will be changed in Q5.3 and you could change it for the moment in the file CoreDescription.aslx in function ShowRoomDescription.
Look here: viewtopic.php?f=10&t=2921&p=20065&hilit=ShowRoomDescription#p20059