New game has it too...very strange. Abot, since you're very intimately familiar with the Windows Glow mods, is there any way a script may have been broken unintentionally? By another mod in a load order, I mean.
there are 2 script changing windows state, max_common_window_01 should enable _01 type windows at daytime, max_common_window_02 should enable _02 type windows at night.
if you see a _01 type windows at night or a _02 type window at daytime, something is probably not working as expected.
try a fresh new game (so you are sure to be testing mod problems, not save game problems) with just Windows Glow.esp loaded, if it works add another mod from the list
1 Windows Glow.esp
2. abotwindowsglow.esp
3. Windows Glow - Tribunal Eng.esp
4. Windows Glow - Bloodmoon Eng.esp
5. Windows Glow - Raven Rock eng.esp
and so on, you may find the problem if it is a mod
A fast way to get mod list in proper loading order is from Mash saves tab, click a save, right click the File header on left column, copy list