Adobe Media Encoder Rendering Issues

Ok so I am using Adobe Media Encoder version 7.2.2.29. I have been having issues with encoder for awhile now. When I go to queue my videos the encoder doesn't render the file correctly either it be like the example below where a simple imported logo into premiere looks completely different or updates I make to a AE dynamic link... These AE dynamic links update in Premiere but when rendered in the encoder it doesn't update. So I have been having to export in Premiere for each video which is wasting a lot of time.
When exporting I am using different presets to see if that would fix the problem first a Youtube 1080p 23fps preset then a Vimeo preset still same problems. 
What is going on how can I fix this.
Thank you,
Logan

A higher quality queue doesn't work... match source hit bitrate, pro rez nothing seems to work. Also using a higher quality export doesn't fix the issue of why Adobe dynamic links aren't updating in the encoder...
Direct export from premiere works but like I said above it is a huge waste of time. I pump out multiple videos a day with multiple re-edits so I need to work while exporting. So while it works it is not a solution that will work for my situation.
Thank you,
Logan

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