My guess is that you have placed them in empty openings. This can confuse the poor columns (which aren't all that bright) as they may think they are in full height walls and not fully understand that there are holes in the wall.
If this is the case, you can split the wall into three sections. Two full height on either side of the opening with a high wall (on a layer which is hidden in the floor plans) to form the head of the door.
Another choice is to use library parts for the columns. They are oblivious to the presence or absence of walls and openings and so will display correctly in plan and 3D regardless.
The column tool has always been a bit troublesome. When introduced back in AC5 an understandable but unfortunate decision was made regarding the columns' relationships to walls. Since the wall already existed (since the beginning) the column was designed to be modified by the wall instead of the other way around (it was presumably easier to write the new element to adapt to the existing one rather than rewrite something so integral to the program as the walls in order to accomodate the new columns.
One result was that in 3D, columns are the elements cut away rather than the walls. For example, a large tall concrete column with a lower partition wall drawn through the center will create a slot through the entire height of the column. Another case recently discussed in this forum was of columns embedded in low walls which disappeared entirely.
Now that there are solid element operations we can hope that the columns will become able to behave properly in 3D. Proper clean up in plan may be a bit trickier.
Rubia Torres
