Sounds like you’re doing everything correctly, but one thing I would suggest is to try and run the Plan Generator with just a Level 01 and Level 02 – disregard Level 00 as this would only be used if you have full sub-level floor represented as opposed to a foundation plan. Our scenes will automatically account for the depth of any ‘ELEMENT – Foundation” geometry.
Also, be sure you have the appropriate drawing set loaded up before you run your scenes. This can cause issues with certain items not being represented correctly.