Premiere Pro not understood by Media Encoder properly

When I am in premiere pro I have a PSD layered file that is animated on the time line as a lower third. Everything in the timeline is fine. If I export and encode from premiere pro it encodes fine. However, if I send to queue and encode in adobe media encoder it encodes changing the scale of the psd layers from the image back to the original position of the psd. This seems like the encoder does not understand the latest update in Premiere properly. Anyone have any ideas or a way to resolve this on this end? (Below are two images one is showing the lower third PSD from within premeire, the other is showing what the media encoder is doing to the PSD lower third)
Thank you for any sugestions.

Hi MRJay,
I had a similar issue only when using 3rd party plugin (Creative Impatience) that would go all catywhumpus on Encoder Queue outputs...it would mess with certain images or text that were not necessarily matching the project proportions (e.g. crop them, or ignore 1/2 of my Feathered Crop, etc.)
The solution was bizarre, and likely source-code default setting based...
After going to Media-->Export and when in the Encoder interface--before Queueing-- find a section on your timline with the scroll controls where the graphic is, make sure you are in Source Tab (top left), goto Crop Proportions; Use the drop down tab to actually set the Output dimension to what your sequence is (you won't have to actually export with this setting) and then switch to the Output tab. Does it now appear correct? That's it...undo the Crop Prop. and output normally. Hope this helps...

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