Transparency is a little quirky, the two options that work for me:
1. the easy method make the glass a separate model and add it in the editor (not my preferred way)
2. Make the Glass a separate group in the X file and set transparency = 6 in fpe (this is the way I currently do it and have had very good results)
Welcome to the real world!
Main PC - Windows 10 Pro x64 - Core i7-7700K @4.2GHz - 32GB DDR4 RAM - GeForce GTX 1060-6G 6GB - 1TB NVe SSD
Test PC - Windows 10 Pro x64 - G4400 @3.3GHz - 16GB DDR3 RAM - GeForce GTX 950 2GB - 500GB SSD
Laptop - Helios 300 Predator - i7 7700HQ - 32GB - Nvidia GTX1060 6GB - 525GB M2 - 500 SSD - 17.3" IPS LED Panel - Windows 10 Pro x64