As much as I complain about Apple codecs and Adobe products, occasionally a bug comes up that is truly mind boggling. Take Prores 4444 and alphas: “if the first frame has no alpha, then nothing passed it will have an alpha either”. Thanks, Apple and Adobe!
This problem was solved in After Effects by creating a 1×1 pixel mask on the first frame of everything rendered using Prores 4444. The mask moved out of the way after the first frame, and the alpha channels rendered intact for the rest of the sequence. It’s all voodoo, voodoo I tell you!
This bug was reported May of 2011 and nothing has been done yet (most likely because Adobe engineers threw up their hands and blamed Apple).
On a side note, this is frustrating because I like to use Prores 4444 to convert EXR sequences after rendering but before compositing (if the EXR’s only contain rgba information). Taking 70gb of EXR’s down to one 2gb nearly-lossless Quicktime file is a pretty good trade off. Except when the Alpha doesn’t render.