I know you say it is not a renovation issue, but check the renovation status of the wall and door.
You will probably find the wall is 'existing' and the door you are placing is 'new'.
If I place a 'new' renovation status door in an 'existing' renovation status wall, I get what you are getting.
When you model a new wall its renovation status is 'new' and the door is also 'new' which is why they appear as you expect.
Use the Renovation palette to set the status of elements you will be placing.
Because you are using a renovation filter that 'shows all elements', you will find the 'existing' wall shows and the 'new' door shows as well.
So technically, it is doing exactly what you have told it to do.
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