So this morning I had the opportunity to speak to guest services about my email.
Firstly, to everyone else on here who has also recently stayed and had an issue with a staff member either knocking or entering the room with the room occupied sign up - Disney want to hear from you. I mentioned I had seen reports from others on here and on trip advisor and they requested that I ask those that had a similar experience to email them directly and provide the details. They are working on refining the policy (they know they have issues), but to do so they need to hear from people about what is and is not working.
Secondly, he told me that they are moving to a system where if house keeping or security come to your room and the room occupied sign is on the door, they are to have the resort send you a text message. The text message then requests you let them know what time would work for you. Cast members have been instructed NOT to knock if the sign is up. To be honest, I think the text message policy is probably the least intrusive option and therefore best way forward (a text message is easier to sleep through than a ringing phone!). He also confirmed what others have mentioned here, which is you can specify a window with the front desk for your room to be entered if you prefer it to happen at a specific time of time.