Alpha Channel / Media Encoder Question

Hello All,
I have a question that I think is just something I'm overlooking. I have a Comp with a logo. The logo is made up of various files and does not have a solid background. It's very similar to a lower third.When I render it out in AE via the Render Que I have no issues and the Alpha channel works as expected when imported into PPRO. The setting I use is QuickTime>Animation>RGB+Alpha, etc.
This morning I decided I wanted to start rendering via Media Encoder. I watched the video Colin Smith did a bout a year ago to refresh my memory.
I fired up Media Encoder, dragged my logo comp into ME and everything seemed to being going beautifully. I chose QuickTime> Animation codec>etc.
However when imported the file into PPRO the Alpha channel did not render. Where the Alpha channel is supposed to be PPRO read as black video. I went back in ME and doubled checked all of the settings. I do not see anywhere in ME where you can specify an Alpha channel as you can in AE where you can specify "RGB+Alpha".
Is there a setting in ME to activate/read the alpha channel that I'm missing? I'd really like to use ME for future AE comp renderings but unless I can get around the Alpha channel issue I won't be able to.
CS6 all up to date
Win Vista (not that I think any system specs matter in this instance).
Thank you in advance,
Shane

From AME, add the file to the render queue and click either the codec or preset to open the After Effects export settings. Under Basic Video Settings selecting a Depth of 32 bit will enable the alpha channel. If using a 10-bit or greater codec, set the Depth to 64 bit.
As an aside, have you considered creating a Dynamic Link from Premiere Pro to the After Effects file? It eliminates the need for an intermediate file and allows you to maintain a bit depth up to 32bpc.

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