Ok, so I was browsing my files and noticed that the settings in My Documents/Games/Skyrim/skyrimprefs.ini were different that the same file in my x86 folder inside steamapps/skyrim folder. The first thing I noticed is the difference in shadow settings. I've posted before about how the shadows have never worked correctly again since the .exe patch that happened several days back. I've never seen this particular issue posted about and I am wondering if this may be the source of my shadow problems. I dont' know how to fix this, but I can say that no matter what settings I use in options on the splash screen, they shadows don't change in game at all. I can't make them worse and I can't make them better. I have a good machine and the shadows were working good on ultra settings before the patch.
So, with explanations out of the way, I have a thought and a question. My thought is, when I change my settings on the splash screen, it does change the .ini in the prefs ini that is located in My Documents, but it does not change the settings in the ini with the same name in my x86 files. My question is, why the hell to I have two of these in different locations in the first place? Why does the game change the settings in one, but load the other when it starts up? Here's a copy and past of a port of each:

My documents version:
[General]
fBrightLightColorB=1.0000
fBrightLightColorG=1.0000
fBrightLightColorR=1.0000
iStoryManagerLoggingEvent=-1
bEnableStoryManagerLogging=0
[Imagespace]
bDoDepthOfField=1
iRadialBlurLevel=1
[Display]
iBlurDeferredShadowMask=3
fInteriorShadowDistance=3000.0000
fShadowDistance=4000.0000
iShadowMapResolutionSecondary=1024
iShadowMapResolutionPrimary=2048
iShadowSplitCount=2
iMaxAnisotropy=16
fLeafAnimDampenDistEnd=4600.0000
fLeafAnimDampenDistStart=3600.0000
fTreesMidLODSwitchDist=5000.0000
fGamma=1.0000
fDecalLOD2=1500.0000
fDecalLOD1=1000.0000
fSpecularLODStartFade=1500.0000
fShadowLODStartFade=200.0000
fLightLODStartFade=3500.0000
iTexMipMapMinimum=0
iTexMipMapSkip=0
iWaterMultiSamples=0
iMultiSample=8
iShadowMode=3
bTreesReceiveShadows=0
bDrawLandShadows=0
bFull Screen=1
iSize H=1050
iSize W=1680
fMeshLODFadePercentDefault=1.2000
fMeshLODFadeBoundDefault=256.0000
fMeshLODLevel2FadeTreeDistance=2048.0000
fMeshLODLevel1FadeTreeDistance=2844.0000
fMeshLODLevel2FadeDist=10000000.0000
fMeshLODLevel1FadeDist=10000000.0000
iScreenShotIndex=2
bShadowMaskZPrepass=0
bMainZPrepass=0
iMaxSkinDecalsPerFrame=10
iMaxDecalsPerFrame=30
bFloatPointRenderTarget=0
sD3DDevice="NVIDIA GeForce GTX 560"
bFXAAEnabled=0
iShadowMapResolution=2048
fShadowBiasScale=0.2500
iShadowMaskQuarter=4
iAdapter=0
iPresentInterval=0
iShadowFilter=3
bTransparencyMultisampling=0
bDrawShadows=1

Now here is a copy of the same lines from the x86 version:
[General]
fBrightLightColorB=1.0000
fBrightLightColorG=1.0000
fBrightLightColorR=1.0000
iStoryManagerLoggingEvent=-1
bEnableStoryManagerLogging=0
[Imagespace]
bDoDepthOfField=1
[Display]
iBlurDeferredShadowMask=5
fInteriorShadowDistance=3000.0000
fShadowDistance=2500.0000
iShadowMapResolutionSecondary=1024
iShadowMapResolutionPrimary=2048
iShadowSplitCount=2
iMaxAnisotropy=8
fLeafAnimDampenDistEnd=4600.0000
fLeafAnimDampenDistStart=3600.0000
fTreesMidLODSwitchDist=3600.0000
fGamma=1.0000
fDecalLOD2=1500.0000
fDecalLOD1=1000.0000
fSpecularLODStartFade=500.0000
fShadowLODStartFade=200.0000
fLightLODStartFade=1000.0000
iTexMipMapMinimum=0
iTexMipMapSkip=0
iWaterMultiSamples=0
iMultiSample=0
iShadowMode=3
bTreesReceiveShadows=0
bDrawLandShadows=0
bFull Screen=0
iSize H=900
iSize W=1600
fMeshLODFadePercentDefault=1.2000
fMeshLODFadeBoundDefault=256.0000
fMeshLODLevel2FadeTreeDistance=2048.0000
fMeshLODLevel1FadeTreeDistance=2844.0000
fMeshLODLevel2FadeDist=3072.0000
fMeshLODLevel1FadeDist=4096.0000
iScreenShotIndex=2
bShadowMaskZPrepass=0
bMainZPrepass=0
iMaxSkinDecalsPerFrame=3
iMaxDecalsPerFrame=10
bFloatPointRenderTarget=0

Notice the difference in screen resolution and also the fShadowDistance. I have no idea what these numbers mean, only that they are vastly different and that the game hasn't looked as good since the aforementioned "patch". Could this be the source of my issue? My monitor is a 1920x1200 monitor, which is what I was playing at prior to all this happening. Where the hell would the game pull 900x1600 from? Could someone that knows about this stuff tell me if I should manually change the x86 version to match the version in My Documents?

It's probably just the template that is used to create the one in My Games/Skyrim if it doesn't exist.