Hello,
On the Build Roof Dialog you have the option for either Retain Manually Drawn Roof Planes or Retain Edited Automatic Roof Planes.
The first option (Retain Manually Drawn Roof Planes) will affect any roof planes that were drawn manually by using the Roof Plane tool. This tool can be found by going to Build> Roof> Roof Plane. You can tell if a roof plane was manually drawn because it will show “Manual Roof Plane”, like it shows in your screenshot.
The second option (Retain Edited Automatic Roof Planes) will affect any roof planes that were generated by the Auto Rebuild Roofs or the Build Roof Planes option, and then were manually adjusted or marked as edited. A roof plane will automatically have the “Mark as Edited” checkbox enabled if you made changes to the roof plane after it was generated. (ie. Changing its’ pitch, reshaping, repositioning, etc.).
You can certainly have a mix of these roof planes in your file. You can have the ones that were automatically generated by the Build Roof tool, but you could also have some that you manually drew in using the Roof Planes tool. Based off of your screenshot I'm thinking you might have group selected your roof planes. I would instead go one by one and take note of "Mark as Edited" or "Manual Roof Plane".
I hope this helps!