Glad you solved it. I consider the behavior that you've seen a bug and have had it bouncing around the system for several years now, waiting for someone from GS to believe me.
When you place a door or window, you have two anchor points for insertion as shown in the attached. The "Anchor Point" is the 2-D insertion and has no real meaning in how the object behaves - same as picking a hotspot for an object for placement.
The "Anchor" - sill or header - effects the appearance of the object in section/3D as it determines the wall thickness used by the window/door by "reading" the wall thickness at that vertical position.
So, adding base trim, or holding up the gyp, etc. - anything that makes the base of a wall not the same as the main face, results in the door trim either pushed into the wall surface, or floating off of it if the anchor is the sill and the sill is located in the effected areas (as it would be for a door).
Graphisoft's "solution" is to use the door Header in this situation as the anchor. Well, that only works if the header happens to be align with the main surface of the wall.
The purpose (supposedly) of the opening reference lines that we place in the Profile Manager is to specify where we want windows/doors oriented. These lines are ignored (1) in the situation above, and (2) with respect to the thickness of the wall - that is, only the reference line on the insertion side is recognized - the line on the opposite side is ignored.
This mostly annoying situation can generally be worked around for conventional construction such as your walls by switching from header to sill/etc.
But, I recently worked with a client doing custom log homes and found that there is no reasonable solution for profiled log walls! If you model a stack of logs of different diameters to get a more natural look to sections, you find that inserting a window or a door is impossible: if the sill and header happen to be where the logs meet and the wall is thinnest, the trim is inset deep into the walls. Wall opening reference lines provide no mechanism for defining the desired thickness of the wall so that proper depth bucks will be generated with trim at the desired location relative to the log faces.
(The only workaround would be what you did: magic wand a white fills to fake a flat surface to the outside/inside of the log wall - at a high polygon count cost - and assign that mass a 100% invisible material for rendering purposes.)
Has been a real sore point for me for years, so sorry for venting!
Cheers,
Karl
One of the forum moderators
AC 28 USA and earlier • macOS Sequoia 15.2, MacBook Pro M2 Max 12CPU/30GPU cores, 32GB