This is happening because the ground where you are placing the building is not flat.
Either it is on a slope or there is a slight rise somewhere in the area of placement.
If you place your building in the editor, you can then use the init field for the building to raise it slightly.
However, depending on how much you have to raise it, you may come across another problem......from the outside you might find one or two edges of the building are floating a few centimetres above the ground.
Anyway......
buildingname setpos (getpos (buildingname select 0), getpos (buildingname select 1), getpos (buildingname select 2) + X)
or
this setpos (getpos (this select 0), getpos (this select 1), getpos (this select 2) + X)
Syntax may be a bit wobbly.
X of course is the height to raise it by.
You will have to experiment till you get the height you want.......start with something like 0.5 and work up or down as the case may be.
Planck