same preset, same video source, different video qualities from short clip test vs full length

Hi All,

I used the same preset in Media Encoder 2017 on two files. The 30 second clip looked nice and crisp and the full length 78 minute clip looked significantly less. Does anyone know what could have caused this?

Source material is recorded Red One and it is 3840x2160 at 23.97 fps.

Computer Setup:

OSX El Capitan

Mac Pro (early 2009)

Processor 2 x 2.93 GHz Quad-Core Intel Xeon

Memory 16 GB 1066 MHz

Graphics ATI Radeon HD 4870 MB

Any suggestions would be greatly appreciated. I would like to find out if it's an issue with my machine somehow, or just a few settings that need to be tweaked

Thank you!