Media Encoder green artifacts

I met a problem when I encoded a video with Media Encoder (I work with Adobe CS5.5 on Mac) : at first, when I encode a video on Premiere Pro, the rendering is OK. But when I want encoding this video with Media Encoder, some green artifacts appear on the video. I don't know why. Can you help me ? Thanks for anything help.

Hi Kevin. Thanks for answering. Below here some details :
I work with Premiere Pro sc5,5 (I updated 5.5.2 version after recommendation. I did it too for After cs5,5 and Media EncoderCS5.5, but without improvement). I run with OSX 10.9.5 (MacPro 5,1).
Graphism : ATI RADEON HD 5770 1024 Mo.
Processor :  2 x 2,4 GHz Quad-Core Intel Xeon
Memory :  16 Go 1066 MHz DDR3 ECC
Here's the problem : when I export my video with Media Encoder at from of Premiere Pro timeline, a video exclusively made on After Effects with the plug in ELEMENT 3D (from VIDEO COPILOT), the export is (long but) well and the video is clean. But when I want to use this new exported video with Premiere Pro ( I usually do this when I have a big sequence with a lot videos. In fact, I use this "process" to avoid a long calculation of my computer ), it appears some green artefacts on it. Artefacts (below) which not appear when I looking at it with Quicktime, for instance..
This is the first time that I met this problem.

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