@Pirate Myke
The procedure I use is to create the building model in my modeling software and save the model. After saving I then import a separate model file just containing the windows. With the proper settings in the fpe file, this process works 100% of the time in the real time mode. All windows function as intended. What is making me somewhat upset is, any model using transparent windows, when light-mapped is all messed up. What I am trying to get confirmed is a possible bug in the light-mapping process, not any problem with the model. If I never light-map I never have any problem.
It seems to me, that if the creation of the model requires the windows be at the end of the x file sequence (and this works) then to get the light-mapping results illustrated in my post, then mapping is reordering the x file original data sequence. If this is the case then I must abandon making models with real windows because I can not predict how users of my models will use them in their game concepts. If they don't light-map then everything is fine, if they do then the model is a mess and the customer is upset. My personal opinion is that this needs to be fixed sooner than later.
Windows 10,64 bit|AMD FX-6200 Six-core-3.80 Ghz |CPU PASSMARK 6,142 |Memory 10GB |NVIDIA GEFORCE GTX 660 SC |GPU PASSMARK 4,114