So pretty much the color is really off on the encode and I can't figure out why and yes I am a noob at this so I wouldn't advise saying anything without an explanation because then I'll just ask how do I do that

Here are some screens to show what I'm talking about
http://screenshotcomparison.com/comparison/141520
http://screenshotcomparison.com/comparison/141521
http://screenshotcomparison.com/comparison/141522

And here are my encoding settings, the AVS script was nothing special, only put in the Crop and Spline36Resize commands with FFDIndex Source.
http://imgur.com/a/DlyvN#0

Btw if you're confused about the colormatrix setting because it wasn't in the original 4 settings logs then just to let you know I did use bt709 for color matrix, it just wasn't in the first four images cause I did another encode without bt709.