Embedded/linked blocks bug?

Recently I have change my workflow for a massive use of external files. I use lots (some 30 or 40 files) of VA elements built with embedded and linked blocks, both for 2D and 3D representation. And it works, almost. Recently I have came across a problem.
I’m working on a house with some dormers. Firstly, I have put a roof and dormers’ roof in a separate file. It had been working perfectly. The problem had been with dormers’ walls, as I couldn’t make good connections. So, I have moved them to the roof model, and there it looks like this (just as I expect):

All the connections are good, also walls’ extensions. So, the file embedded into a master file looks a bit different (I have switched off all unnecessary elements):

The roof is an element, with external file as a geometry. As you can see, the walls connection is quite messy. The another problem has appeared, out of nowhere, suddenly I couldn’t see some windows. This is the external model:

And this one a complete model:

Would you take a look at this? I can send you files, of course.

Hello @jerry.bakowski,

Yes, please, send me the model and I will take a look.

I see there is a window missing in the last image. Which walls are not connecting as you would expect?