New problem with transparent windows.
attachment 1 shows the subject entity placement with the bottom of the piers sitting on the terrain and the surrounding buildings. attachment 2 shows the view from inside the subject entity with the surrounding buildings fully visible.
attachment 3 shows the subject entity with the bottom of the building piers pushed below the terrain, to the level of the water table. attachment 4 shows the view inside the subject entity looking out through the windows at the surrounding buildings. NOTE: the surrounding buildings have disappeared and only show the missing building shadows and the portion of buildings seen thru the open door way.

If I tab, tab and turn the water and reflections off, the buildings then show through the window glass as in attachment 2. What in the heck is the connection between the window glass and the water table?

Put all the buildings on dry land and all of the transparent windows work as designed. Inside or out
The transparent windows are all added as the last element in the "x" file

Change the transparency mode to 6.

Here is what each mod number means and does.

// transparency modes;
// 0 - first-phase no alpha
// 1 - first-phase with alpha masking
// 2 and 3 - second-phase which overlaps solid geometry
// 4 - alpha test (only render beyond 0x000000CF alpha values)
// 5 - water Line ( object (seperates depth sort automatically) )
// 6 - combination of 3 and 4 (second phase render with alpha blend AND alpha test, used for fading LOD leaves)
// 7 - very early draw phase no alpha
t.tryfield_s="transparency";

Now also it is a better practice to have the windows as separate object at transparency mode 3. If you dont want to do that then draw the windows objects last in your model, re export it and erase the .dbo file associated with the model and retest it.

Mode 5 has recently been reserve for water only, so that on will not work probably for you.

Have not played with mode 4 before.

I need to be clear about the problem...
The transparency mode is set in the fpe file at "6" and the windows are drawn last. The windows are not the problem. The player can walk into any of the buildings and look out thru any window and see everything there is to see as long as all elements are on dry land. The buildings with windows are just like the real thing, nothing is removed from sight. If you take any building with working windows and you place any portion of the building in the water (such as piers as part of the entity) the objects that should be observed thru the windows will go away leaving just the shadows on the terrain. If the building touches the water or is pushed down to the level of the water table on dry land , the same lousy thing happens.

When the building with piers (shown in the attachment in previous post) has the piers in the water or is pushed down to the non visible underground water table then the objects that should be seen are gone, leaving the shadow where the building should be. While standing in the subject building looking thru the window that shows no buildings that should be seen doing a, tab, tab and setting the water shadow/reflection to "0" the buildings pop into view like magic, changing the shadow/reflection slider to anything other than "0" makes them go away again.
move the same building out of the water or raising the piers to the level of the exposed terrain everything works just as it should. I have all of the required settings for putting see through windows into building, I believe they are correct and work.

As you know, setting the water/reflection slider to "0" makes the water disappear revealing dry land, thus the obvious conflict between windows and water is exposed.

When I have the time I will try to illustrate the problem with a video. My intent is not to solve the problem but to bring it to the attention of others who might be interested. I'm sure over time lee will fix the problem.

Turns out, (after a lot of screwing around) the problem was with the pier model not GG. Rebuilt the pier model and the problem disappeared. The only problem left is, I have no idea what I did to fix it. As is the usual case when I run into this kind of graphic glitch it is my own fault rather than GG.

Excellent. Glad it is working for you now.