Opacity not exported

Have you tried using the After Effects Render Queue instead of Adobe Media Encoder?  The file will be very large and may not play smoothly, but try "Best Settings" for the Output Module and "Lossless" for the Render Setttings ("Lossless with Alpha" for the Render Settings if an Alpha is required).  Assuming that each frame appears as expected in the resulting file (opacity changes included), add that movie to Adobe Media Encoder. 

If you rendered with an alpha, you may need to render two passes (one RGB and one Alpha only) if the format being used in AME doens't support an alpha.

The (slightly handwaving) explanation:

All video encodes the pixel colors in each frame using channels, either red-green-blue (RGB) or luminance-chrominance (YUV). Those 3 channels only define the color, not the transparency; for that you need a fourth 'alpha' channel. Since it's impossible to record alpha with a video camera, nor display it on a TV, all the 'consumer' video formats like H.264 stick with 3 color channels to make the files smaller and the processing easier. Video codecs that have the 4th alpha channel are either designed for a very niche application (such as Quicktime Animation, an ancient format created for doing graphic overlays like the lower thirds on TV news) or they are designed as high-end "mezzanine" formats for post production (such as ProRes 4444, or EXR image sequences) that have massive data rates to preserve every ounce of quality. You have to choose either a rarely-suported codec, or a monumentally huge file.

But, since you can't play a transparent video to an audience, whatever you want this for it's eventually going to be composited over something else then encoded to a delivery format, like H.264. Now all the transparent pixels are full of background, there's no alpha channel any more. A huge file that never leaves your computer is no problem.

If you are sending the video to someone else for compositing (e.g. selling lower third animations to a TV station) then ask them what they want, and supply it. If that means posting hard drives instead of uploading a link, so be it. They're paying.

From the way you write, the new forum should be just what you want ("like some kids messaging service").

Back to topic.

The issue is not opacity, but alpha. You rendered the comp in H264 codec which doesn't supprt alpha. Render your comp as image sequence, DNxHD, ProRes or any other codec which supports alpha.

*Martin

To help we need workflow details and screenshots. Have you spent any time at all going through the tutorials Adobe provides on the AE Product page? Learn & Support or even easier, check out the Home screen in AE.

It also sounds a bit like you are using After Effects to edit a movie. It's the wrong tool for that. AE was never intended to be used to edit. After Effects is a motion graphics application designed to produce visual effects and motion graphics that cannot be produced in an NLE. Short sequences are ok, but editing in AE is a real time-waster. 

Give us some details and we can probably help. I will tell you that if you use the standard templates for comp size and frame rate and choose the standard templates for rendering with either the Render Cue or the Adobe Media Encoder, everything you see in the composition panel's Active Camera view will show up in your final render unless you have added guide layers or expect the composition background color (remember what I said about custom settings). Don't crop your screenshots and show us everything you modified in the layers that are giving you problems by selecting them and pressing the "u" key twice, then PrintScreen and paste to the forum.

Hi,

Need some clarity please.

1. Are you wanting a video render with transparent background areas?
2. What format are you rendering to?
3. How do you intend to use the video? eg Youtube.