Seems like there is a bug with the other versions with the same issue, on both exe and sh versions. loading an old save that is past the door is a good way to get around the issue temporarily.
Viewing post in Version 0.5.1b Update comments
This is a bug related to a new setting called Persistent Markers. Enabling it will permanently resolve the issue, even if you subsequently disable it. First-timers won't have a problem with this, but those who've played an older version may experience this. But don't worry, I'm already working on fixing it.