The hole that the skylight is cutting in the roof shows not perpendicular to the roof edges contrary to the rest of you drawing. This is a common problem with lower slope roofs.
Select the roof and with your mercedes cursor on an edge of the skylight hole.
Click and select the top right button of the pet pallet "set roof edge angle" and change it to the angle you want. Use the 'apply on all edges' if appropriate.
This may or may not solve your gray blob setting.
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"