The picture shows what I mean. The smoke on the right building is not above the chimney, but on the chimney.
smokeoffset.png
The smokeoffset for this building is (0,3), i.e. the smoke is put on a tile outside of the building. That tile is flat.
Smoke offsets larger than the factory size should not be used, those could lead even to crashes.
EDIT: Simutrans now corrects wrong offsets on loading time and writes a warning to the log in r11777.