In order to narrow the problem down I decided to remove all effects and add them one at a time under [EFFECT]. I came across some interesting results. These are the settings that directly affected the sky to cause the problem I am reporting. (I am not entirely convinced though that these effects are the only causes).
1. I could not disable EnableSkylighting or EnableCloud Shadows. With only both of these enabled, the color of the sky was actually slightly bluer than the reflection.

2. Enabling both Mist and especially Volumetric Rays causes the sky to become significantly lighter with my current settings. This was the reason I needed to add filter colors for the sky to begin with.
The color changes associated with these settings are not reflected in the waterMIST:

VOLUMETRIC RAYS:

3. Enabling water causes the image reflected on the water to become darker (at least with my current settings)

Of all these, the issue with volumetric rays is the most troubling because its drastic bleaching effect on the sky at high levels is what necessitated me using gradient color filters to begin with. Are volumetric rays supposed to affect the entire sky color?
Here are my settings:
Code:
[VOLUMETRICRAYS]
IgnoreWeatherSystem=false
Quality=2
IntensitySunrise=0.06
IntensityDay=0.06
IntensitySunset=0.07
IntensityNight=0.07
IntensityInteriorDay=1.0
IntensityInteriorNight=1.0
DensitySunrise=2.0
DensityDay=2.0
DensitySunset=2.070001
DensityNight=3.0
DensityInteriorDay=6.0
DensityInteriorNight=6.0
SkyColorAmountSunrise=0.3
SkyColorAmountDay=0.26
SkyColorAmountSunset=0.22
SkyColorAmountNight=0.3
SkyColorAmountInteriorDay=0.3
SkyColorAmountInteriorNight=0.3
I am guessing the SkyColor section might be part of the problem here?
EDIT: Nope... the Sky color doesn't seem to have much of an effect. I also tried clearing all the sky gradient color filters (making them white) to see what would happen.
I don't think this is a sky color filter issue. I think the original simlarities were coincidental. I just think that the there is a darkening and saturation issue where blue is affected more than other colors in the water reflection for whatever reason.