Yes, that's true about manually adding the cleaning fee to a special offer. A lesson that a lot of hosts have learned, I'm afraid.
Going back to the new "Check-in" page -- be careful about "experimenting" with the second field of the "Check-in wondow". Unless you really, really want to specify an end-time for checkins (I don't, for example), don't experimentally or accidentally select any of the offered times. According to one host, once you've done that, you can't get back to either an empty field or just the text that was originally there saying "Select a time". And that same host said that AirBnB couldn't/wouldn't make the change for her. I can't confirm that this really happens, because I don't want to test it and possibly mess up my own listing. (Which makes me want to set up a fake listing just for testing stuff like this, which happens all the time. I have a feeling that AirBnB might frown on that, however...)
If that field IS working that way, it's got to be an oversight by AirBnB and will presumably be fixed soon. Meanwhile, beware.