Hi @Among-The-Trees0
Hard to diagnose the issue without seeing the your listing? I work with several Hosts that have 3pm -flexible on their listings. I advise them to manually enter the check-in time in Scheduled Messages, so can't speak to the problem you are experiencing. We just state the check-in time is after 3PM. We do the same with the check-out time just to avoid any issues and don't rely on the shortcuts for that.
On other properties I work with, they do have a specific window for checkin. In this case we also manually enter that time in the scheduled messages just to be on the safe side. For example, check-in between 3pm-10pm. We then add "if you know your approximate time of arrival, please let us know via an Airbnb message."
Of course, if you change the check-in times at a later date, you would have to manually update the scheduled check-in message. Here is an example of how a property with a 3pm-flexible check-in time looks for one of the listings in a scheduled message: