It's not you.
The door/windows are IMHO worse than ever in 12 US library. I don't know about INT versions. As your screen shots show, sill and stool are not scripted correctly.
-The sill thickness is taken out of the window height, not the RO increased.
-The stool does not sit correctly in relation to the other window elements. If you look with the apron off, the side casings extend below the bottom of the stool.
-The stool sits too high causing the gaps.
-If you turn the stool off, the apron shifts down the height of the exterior sill (couldn't find a cross-eyed emoticon)
Even with the updated library issued a couple of months ago, many of these doors and windows are too buggy to use. This is why they included the AC11 transition library. These parts won't take advantage of the new wall display options such as core only, but they tend to be in better usable condition.
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"