@PugLove888 Sorry for the delay and I should have indicated my playing environment at first.
Platform: PC(Win10) / Never used MOD/CC / All EP, GPs other than GP03,08,09,11, SP08,09,12,13,15,16,18, ILK / Current game version 1.88.228.1020 /
Language is now English from '22/05/19, but until then played in Japanese.
That happened in both of language version.
Then about why I thought "created an empty room directly in the basement".
That just simple. 'Cause that's how I usually build my basement. But one day I happened to use the "Basement Tool" in the "Wall & Empty Room" to create a basement, and I get this issue.(In Japanese version)
I saw this post and experienced the same phenomenon myself, so I checked the issue apperes in English version just to make sure it worked and to see if PugLove888's workaround works.
PugLove888, once you make an empty room on the first floor (a 4x4 is sufficient) try to create a basement using the Basement Tool in the manner of overwriting the walls of the first floor room. It will always raise the land around the room.