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Looks like CFE doesn't work with roof crossing height boundries, it's probably something to do with it being a difference in floor level.. moving from ground level to ground +1 (i.e. 2nd floor or foundation level). I did manage to mash up a couple of alternative roof styles but neither really looks that great.
If your raised floor / foundation area is kinda in the middle and you have a complete block of wall placed at ground level running all the way around you may be able to put one giant roof across the whole thing, the only other alternative I found is to put walls up around the foundation area then build a roof on it (might have to lay some floor on top the walls to give you extra tiles to click / drag to to make the roof work). You can delete all the extra floor / walls needed to place the center roof afterwards, but if you want to change the roof again you may have to add them in (unless it's just delete / undo to make them different heights).
I used the Hipped roof on the center raised part, half hipped roof around the side taking them up to the edge of the raised walls and adjusted the height so it looked at least vageuly sensible. It's not perfect and could probably be made better with more experimenting depending on what your structure looks like, I have included some screenshots of what I mashed together. Hopefully it'll help