Well, i was facing this issue and apparently so are many others (Forum Thread). But since there is no Bug Report thread regarding this issue (at least not one i could find) , i thought i would report it here.
Credits go to BuryYourHead707 for determining the bug was triggered by using Eagle Vision.
The Bug :
Even on setting God Rays to high, every time Eagle Vision is used, the setting reverts back to Low.
Its a very annoying bug for sure. I am avoiding using eagle vision as much as I can because of that. I only use it when the game force me to, like when doing an assassination contract. Its super annoying having to pause the game and change god rays back to hight everytime I use eagle vision. Please have this thing fixed asap.