Adobe Media Encoder cuts off video layer when the Ultra Key effect is applied

I am working on a Mac (10.8.5) using the latest verison of Premiere Pro CC. I am using Ultra Key to remove the chroma key background from the "talent layer" and adding a "new background layer" behind the talent video layer. When I export directly from Premiere, the sequence exports as expected. However, I have many sequences, and wish to speed up the  process using Adobe Media Encoder. When I export the same sequence using Adobe Media Encoder, the top half of the "talent layer" is completly cut off:
The issue has something to do with the Ultra key effect because when I remove the effect from the "talent layer" it exports in tact (with a chroma key background of course). Adobe Media Encoder CC is up to date as well; are there any known bugs with Media Encoder CC and the Ultra Key effect in Premiere Pro?
Thanks!

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