Encoding and compression in After Effects (Problems with some colors and some effects))

Hello dear friends,
I would like to export an openning title video for a movie, which is about 2,45 seconds long and 22 GB (Uncompressed)
The footage is 1920X1080.
There are a lot of effects, such as, alpha chanel clips of smoke, explossions and stuff like this.
When I export it into H264, or Mpeg2,4 or avi or H264(blu ray), I get a bad quality encoding in some parts:
I get bad quality in the glow effect I have attached to the titles.
I get bad quality in the clips of smoke (bad color) (tha alpha chanel of the smoke)
Would you hapen to know why only in some parts I get bad quality and not not in the whole footage?
Is it maybe because I chose to export the project only in RGB and not in RGB+Alpha, since my project contains alpha chanel data?
Even if I export the project using Quicktime Animation codec (which is lossless), I get this bad quality (a little better than the previous encodings of course).
I only get a nice encoding when I export the project with Zero compression, but 22GB for a 2 and a half minute clip, is too much...
If somebody has any suggestions, I would be interested....
Thank you!!
Giannis - Greece.

Hello,
I usally export the project totally uncompressed and then I do the final encoding-compression in Adobe Media Encoder but the problem remains.
I have every preferance to "Best" and "High".
Yes, I get artifacts...
About the Gamma problems, where can I select a color profile? In Adbe Media Encoder?
Thank you!
Giannis

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