I found the issue! It seems that in certain cases the second Gaia scene can be ended before it sets the flag. I will patch it right away! thanks for spotting it!
Edit!
Done!
Most likely your corruption value or your friendship value with Malayna! As far as I could tell the bug couldn't occur unless you were in angelic form. And also shouldn't be able to occur if you were locked into a relationship with Malayna.
That said though it's been so long since I made all this it's hard to tell for sure now. Looking back on scripting I did 5+ years ago is a mess. Wahaha.