ProRes codec options unavailable in AE render

I have FCP X, Motion and Compressor
Running Mountain Lion
New Mac Pro 12 core Xeon processors
And I'm using
Adobe CC
It works on my MacBook Pro laptop but not on my new desktop.
I repaired permissions, relaunched.
Only thing I can think of is that I migrated to a solid state drive using Carbon Copy Cloner and zeroed out the factory install of the OS.
Any help or ideas would be a great help and appreciated.
Thanks gang.
Scott

Scott,
Please clarify the problem. It sounds like you are getting the ProRes codecs in AE. Is the problem that:
You are not seeing all of the flavors of ProRes?
The Codec Settings button is not enabled?
Here's what I see:
I have FinalCut's ProRes codecs installed on my 10.7 machine, but not on my 10.8 machine.
On both my 10.7 and 10.8 machines, I see all of the expected ProRes flavors in After Effects CC: Apple ProRes 422, Apple ProRes 422 (HQ), Apple ProRes 422 (LT), Apple ProRes 422 (Proxy), and Apple ProRes 4444.
On my 10.7 machine, the Codec Settings button is functional for all of these codecs. On my 10.8 machine, it is not enabled.
My machines show the expected result. More on that in a moment.
If this matches your experience, then AE and AME are operating as expected.
Why do you need to access the Codec Settings dialog for ProRes in AE? It sounds like you're trying to write interlaced video, which doesn't require the Codec Settings dialog.
To create interlaced video from AE, open the Render Settings and change Field Render to the desired value.
To create interlaced video from AME, change the Field Order in the Video tab of the Export Settings dialog.
Here's why this is the expected result: the difference in how Adobe video apps handle ProRes betwen 10.7 and 10.8 is due to a change we made that allows us to use the ProRes encoders that are built into 10.8. On 10.7, and in CS6 and older versions, we can encode to ProRes only if the ProRes QuickTime component files are installed by FinalCut (or Motion or Compressor). But on 10.8, After Effects CC (and AME CC and Premiere Pro CC) bypasses that requirement and gets the encoders by using an API available via the OS; you don't have to install the Apple applications. The side effect here is that there's no access to the Codec Settings dialog; my understanding is that the 10.8 API doesn't give us access to that (meaning Apple removed it from the native encoder in 10.8).
The Animation codec doesn't enable the Codec Settings dialog, either. Most QuickTime codecs don't, and when they do it is usually a remnant of obsolete workflows. (For example, many eons ago some applications couldn't set the interlacing flag inside of the QuickTime file. The user would be expected to set the value for the codec by using the Codec Settings dialog.)

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