I don't think this is a ghost plan versus Trace issue at all.
Refer to the manuals - version 10 and 11 - read up on the definition of the element's home storey (esp. version 11) and the projection methods for wall (beams, columns, slabs, roofs as well). Elements are storey sensitive, but by default they also change their home storey automatically depending on the elevation they are placed at and how tall they are. Sounds like you need to disable the automatic assignment of the home storey and select it by name.
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