You've likely moved on by now, but I'll answer for anyone else looking.
First, check the elevation of the buildings layer under its properties. Is it on the ground? For me that displayed it floating above for whatever reason, and I had to work with it at an absolute elevation.
Next, make sure your coordinate systems all agree. Actually, do this anyway since it will mess you up later if they don't.
And finally, a problem specific to the 3D Basemaps solution that I kept running into: the layer that you get when you run the 'create buildings' task isn't truly a 3D layer even though it's symbolized like one. Its symbology is governed by a Rule Package that comes with the Solution, and if you accidentally change the symbology (maybe because you want it to be a different color) you will lose the Rule Package and the layer reverts to its true flat self.
To get the Rule Package back, make sure all symbology is reset to default, no outlines and no fill color, and find the 'layers' portion of the Symbology tab, from which you can select 'Procedural Fill' and re-load the Rule Package from your project folder. It's called LOD2BulidingShells.
In order to get a real 3D layer that you can change the symbology of, first complete your building edits with the 'modify buildings' task in the Solution and then run the 'fuse buildings' task, which will give you a multipatch feature class.
