That door has an orientation of -90 in the set file instead of 90. Usually that doesn't matter because the doors have use nodes on both sides but maybe the transition tries to place the PC behind the door instead of in front of it because of this. The walkmesh is okay, but usually I leave about two meters space behind a door because that's how broad a door is. In this tile there's only room for 1.5 meters because of the walkable second story. So maybe the game tries to place the PC behind the door and there's not enough room so they end up on the second story.
Try rotating the door by 180 degrees. If that doesn't work I have no idea what to do about it. There's nothing wrong with the walkmesh.
I changed the door rotation in the set file to 90 instead of -90 now and it will be in the next update.
Not being entirely sure with this, and definitely not having had a physical look at what you are describing, but strictly speaking towards the typed in numbers you folks are discussing... negative numbers behave oddly at various times.
Anytime I had issues like this, I specifically edit the -90 to be 270 instead. This sometimes fixes that sort of issue.
However, some of the other suggestions in this dialog should also help.
I just today found my copy of 3dsmax 8, so I can reinstall that and take a look at things again. But it will likely take me a while to get things re-installed as this computer seems to have a mind of it's own, and also being win 8.1, Microsloth has done some amazing things to make life increasingly difficult for folks that just want something to work as described instead of how THEY think it should be.... THEY being of course, that nefarious THEY party that seems to control the world from behind the scenes.
Anyway, just try editing that -90 to become a positive 270 rotation and see if that helps you any.