The ArchiCAD standard doors are pretty complex so it's hard to say where it might be going wrong internally.
The result is definitely odd. I assume the door shrinks proportionately and is embedded in the wall suggesting both scaling and origin problems. Is there anything unusual in the way you are saving the panel?
If you enlarge the source panel does it get bigger in the door or remain the same?
I scaled the 3-foot wide door panel up to a 4-foot wide door. Saved the Panel as a Custom Leaf 2 (can select the embedded Library or create a Folder, but can not save it to an office library).
I placed the saved leaf in the same 3' x 6'-8" opening. It Worked.
I re-saved the original door panel as Custom Door Leaf 1 and NOW it works properly also. Seems to be one of those elusive bugs.
So for anyone following the Custom Door Panel issue, I have a question about modeling the Mullions.
In modern Doors and Windows the "Mullions" are actually often placed within the Dual Glass cavity. If this is modeled that way the Mullions do not show in the Custom Door leaf.
Is the Answer to make the Mullions "thicker" than the Glass? or can material transparency be embedded in object that allows the Mullion to display in elevation/section views?
If you enable transparency in the elevation view you will see through the glass to whatever is beyond the doors and windows. You can control this (to a point) by limiting the depth but i'm not sure it's worth it.
It's probably best to express the muntins to the face of the glass. If I were programming it I would put 3D lines on the glass but that's a bit of a chore. Perhaps the trick wood be to model glass muntins flush with the panes using a matching but renamed material so it will render seamless but show in elevation and hidden line views.