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What do you see in the way of channels if you open one of the TIFFs in Photoshop?
You will not gain access to the Alpha if it is not the 4th channel in the file or if it is labeled in an odd manner. The issue certainly rests within the app who created the files/ the person who set up the render passes/ whatever. For the time being, creating an action in Photoshop and mangling the files thru it is pretty much your only option - except for RLA, RPF and EXR, AE simply does not see any custom channels.
Dang Navarro - that's a huge plate! :)
Does AE recognize the alpha in the composition? That is, does it see transparency of any kind on that layer? Could need a reboot if it does. If not, it's possible that the file is corrupted in such a way that the metadata says it's mil+, but there are only 3 channels in the TIFF.
Have you opened one of these in Photoshop (especially frame 0000) to see if there's an alpha?
Also - it's odd that you have one frame in your tif sequence
(shouldn't it read: "[0000-0217]")
In AE, while it says Mil+, there is no transparency. But in Photoshop, there's an alpha. These are renders out of Cinema4D, which I never have a problem with.
I wonder if the insane size is causing AE to have a brain fart? I'm doing that because I'm unhappy with the anti-aliasing (it's a field of grass via a fur simulation -- and there's severe flickering out in the distance). So I'm rendering out 4x 1080p with no AA. I'm letting AfterEffects perform AA when I scale it down to normal size.
I'll make C4D render to PSD files and see if that changes anything.