Hi Greg,

The two hexagons highlighted in the picture are not on the same plane as the rest of your curves, 0.03 units out, so they are treated separate in the extrude function
which created 3 solids, that's what your seeing when you say, 2 hexagons are capped.
If you bring those 2 hexagon curves to the same plane as the rest of the curves you will get the result you were after.



Cheers