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So here's a strange one: I've found that if the first frame of a composition is completely opaque (such as using a solid to fade from black) then any QT Movie rendered with ProRes 4444 + Alpha will not include an alpha channel. I've replicated it on multiple machines and triple checked my MediaCoreQTCodecRulesCS5.xml to ensure that it's correct. Here's the steps to recreate this:

1. create a new comp (Project bit depth = 16bpc)
2. create a new solid with the same dimensions as the comp
3. at Frame 0 create a keyframe for the Solid's opacity (Keep it at 100%)
4. move down 5 frames in the comp and create a new keyframe by setting the Solid's opacity to 0%
5. set the work area to 1 second
6. Render a movie using ProRes 4444 RBG+Alpha

The resulting movie will have no Alpha channel. If you watch the movie being rendered with Caps Lock off and 'Toggle Transparency Grid' active, then you can see the alpha channel while the render is going. If you render using Animation Compression RGB+Alpha, it will be correct. You can also replace the solid with footage as long as the first frame of the rendered comp is completely opaque and the issue is still there. Move the solid or footage down in the time line 1 frame so the first frame of the comp has a transparent alpha channel, then the movie rendered from that will be correct. This has only been tested and confirmed on the Mac and only CS5. If anyone can test and confirm the PC CS5 and Mac & PC CS5.5 it would be greatly appreciated.