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Adobe Media Encoder CC 2014 not recognising opacity/alpha values from After Effects

Time:October 11
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Hello, I'm importing AE compositions directly into Media Encoder to output as 'Match Source - Medium Bitrate H.264' files. However Media Encoder is not recognising the opacity values of the layers in AE and the background images are coming out as opaque rather than partially transparent.
How can I resolve this? If I render the movie from AE as a .mov then use Media Encoder it works fine, but that takes a lot more time.
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Can you post screenshots of your comp in After Effects and the result you are getting from AME?
One issue you may be hitting is that AME is not aware of the composition background color. This is a limitation of Dynamic Link; because a primary use case of Dynamic Link is placing an After Effects composition, such as lower-thirds titles, into a Premiere Pro sequence, Dynamic Link ignores the background color of the composition and treats any the background pixels as alpha. In AME, since there is no compositing happening, black is used to fill in the alpha area.
To work around this limitation, place a solid at the bottom of your composition layer stack that is the color of your background.
You're welcome to submit this problem as a feature request: http://adobe.ly/feature_request