hey, to clarify, the floor is in the right place (or set in the right place, after adjusting in the options menu) but the cubes are all up in the air?
Are the walls high/detached from the ground as well?
Rather than try to find the root of what is causing the issue, I'm gonna write a script that just checks to see if the cubes are level with the ground after you load in, and then adjust them. . I'm very, very sorry that this issue is stopping you from being able to use the program properly... Been aware of this issue a while but for me it was usually only an inch or so of height difference, which seemed acceptable.
Expect an update early next week, Tuesday or Wednesday.