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I have had a problem for some time with pre-baked images not working well with transparent glass. It turns out that these entities really do work but the light-mapping system just fails to display the correct image image at the end on the process. The attached video can shed some light on the problem.

When you move the entity it will lose baked mapping and revert to real time shadows. I don't see any difference in your house when you change to real time after moving it,so I can see it has lost the bake. If you do this in a populated map youmay lose all lightmapped shadows and corrupt the .fpm.
What I have found best is to make any entity's I don't want lightmapped dynamic and after bake set them back to static (real time and lightmapping will show at same time as you can see when you change shadow strength which only affects real time), this is particularly important for entity's which are snapped to grid and prevents any loss of all baking.

For any indoor lightmapped scenes I tend to turn shadow strength down to zero so I get only lightmap shadows and no sun dynamic shadows, this of course defeats the purpose when you want character shadows indoors which are cast by dynamic sunlight. So I am pretty certain baked aren't affected by shadow strength. When you upped the strength in your video you are actually 'overlaying' the dynamic shadow onto the baked shadow, hope this all makes sense.
You could test this yourself by putting a static light in the scene from a different direction and notice you get a different shadow cast when you turn up/down the shadow strength after lightmapping.

I agree it would be nice to have per entity lightmapping, but I cant think of an easier or quicker way than simply changing to dynamic/static even if it were a flag in entity properties since I tend to avoid too many dynamic entity's in a finished build. Might make it simpler for new users all the same

Of course none of this helps if you intend to sell in the store so the transparency with lightmapping issue needs to be sorted properly since it does appear to to be changing the draw order in some way..

@rolfy
You are right. I have not got pre-baked shadows or working windows. I did a poor job of interpreting what was going on. This has reached a point that I have lost all interest in creating models that contain transparent glass. If I have models in the store that have semi-transparent glass that looks good in real-time but goes to h-- in a hand basket it's not worth the trouble. Some how I need to notify users of my models that light-mapping said models does not work as intended.

Thanks for the catch.

I wouldn't give up on it just yet, maybe a fix is not too far off Meantime you could make such media dynamic by default to prevent any issues.

If you want to continue with transparency in your models, please do send me your latest model with FPE and I can take a look and offer some advice. I have had a model showing this problem and it was due to the transparent mesh not being separate from the non-transparent mesh which is vital for the light-mapper to determine a render order.

I still can not figure out the problem with real_time transparent glass let alone light_mapped glass. Lee indicated I was having a problem because my model in question, did not have 2 separate mesh elements, which seems to be a prime requirement.
After creating a model that meet the requirement , I found it still did not work as it should. I decided to remove one of the elements from the equation and have created a model that has only the transparent element (glass) for further testing.

The fpe file contains a transparent setting of "6" , which one can see by the screen shots, does reproduce the transparent texture, glass with holes. The problem is, depending on the users viewing location, the transparency is all screwed-up.
The model contains only 1 mesh and the fpe file forces it to be transparent. (I have also tried an fpe setting of 3 with the same results)


The view looking north, I can see all 4 window panels and the holes this is how it should look from any viewing location.


The view looking east, I can only see the holes in the north and west panels


Looking south, I can only see the hole in the north panel


Looking west, I can see only the west, north and east holes in the panels

I will send Lee a new model when I can but I worn out for now. (I still think the problem is with GG but I am not an expert) maybe someone might try the same, using different modeling software, mine might be part of the problem (AC3D)

Not sure if this is related it seems so. Using the Poly Tunnel object out of the sci-fi pack you can clearly see grass from one angle and none from the opposite side. The glass is also easier to see through, you could put it down to your shadow blocking the glare of course I'm pretty sure it is not intentional as such, just how the shader works.

I have asked the author of the glass test for a model with four meshes, one for each pane, and I will see if the engine can draw in distance orde which should solve the issue.