are your windows subpatched? If they are when you merge points this will cause some geometry issues that will make these problems.
There are two solutions:
1) Freeze the glass texture
2) Do not merge points after creating the air texture.
Also make sure the smothing settings are the same, if your using 89.9 in the glass texture then make sure your using the same in the air texture.
I hope this help if not let me know.
-Lee
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