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I'm using NVR and VisualV and I figured out what the issue was.

I followed the instructions at the bottom of the ReadMe that tells you how to make them work with PRSA. However, in step 3 at the bottom it says to open timecycle_mods_2.xml, but I only have 1,3 & 4 in that directory. For some reason, between the instructions for intsalling the weather mods and the instructions for installing PRSA, certain files ended up in two different directories, the GTA V root folder and mods folder.
For step 3 in your Readme, it says to find timecycle_mods_2.xml inside of
update/update.rpf/common/data/timecycle/timecycle_mods_1.xml.
Maybe I misunderstood, but it appears you meant Grand Theft Auto V/update, which is where I looked. Perhaps you meant Grand Theft Auto V/mods/update and I misunderstood. In any case, after editing the timecyle_mods_2 that is mods/update.... It finally worked outside of the pause menu.

I wonder how many people don't realize that it's not working properly because the videos on youtube of PRSA working, the graphics look much worse then how mine currently due. Their's look like mine did when it was only activating in the pause menu.

Example - https://www.youtube.com/watch?v=O012WnQSv24 (This is how mine looked before I got PRSA to enable).

Here are two examples of before and after...now it looks 100x better.

Here's how it was looking before unpaused -
https://imgur.com/XrUCizm

How it would look after I paused the game (besides the obvious lighting changes, notice the geometry changes, especially the poles)

https://imgur.com/wcy64OZ

Now how the game looks after editing timecyle_mods_2 in mods/update...
(PRSA + VisualV)

https://imgur.com/7yPowjo

(PRSA + NVR)

https://imgur.com/qeKUuX1