MSAA/SSAA not being applied, per-game .INI

[ArecaidianFox]

I cannot seem to get Dolphin to apply MSAA/SSAA on any game through the GameSettings .INI files, at either "*\Documents\Dolphin Emulator\GameSettings\" or "*\Sys\GameSettings\" location. I am fairly certain I have the vales set correctly, and indeed the yellow notification text that appears when loading a ROM states that the values are being "overridden by game ini." Here's a sample of the MSAA and SSAA settings from one of my .INIs;

[Video_Settings]
SSAA = True
MSAA = 3

Using Dolphin's main graphics configuration menu and setting a global value for all games actually solves the problem, but that defeats the point of having per-game .INI files. Any help sorting this out would be appreciated.

Dolphin 4.0-9135
CPU: Intel Core i7-4770K
GPU: EVGA NVIDIA GeForce GTX 970
RAM: 8GB