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Well, it pretty much tells you what's going on - you have exceeded the number of channels in your RPF/ RLA file. As per the original RLA/ RPF specs, a given maximum channels are allowed (either 8 or 16 ID channels for instance, if I recall correctly) and the files must be 8bit or 16bit. AE does not support later revisions of those file formats where Autodesk expanded some of these features and included support for 32bit/ float. They never documented those additions publicly, so short of extensive reverse engineering there is no way for others to support these features and that's what you see. Lesson learned: Always render to EXR or separate sequences. You will have to mangle your existing sequence through some sort of conversion, e.g. in fcheck, if re-rendering is not an option.
Ok, if I understand you correctly there is a limit to how many channels AE can read from an rpf file. But I only had two "extra" channels (at 8bit), zdepth and Object ID in the rendered sequence.
I did a re-render last night at low quality and the problem is gone. Since the original sequence was rendered on different computers some of the information probably did'nt render properly later on in the sequence. I checked individual frames in the original sequence this morning and some of the frames was missing the channel information.
Confusingly, it seems AE only displays channel information about the first frame in a sequence (in the Project panel).
Thank you for making things clearer though and I'll look into the EXR-format since it seems to be a safer alternative.
I see... A mismatch in the channel count would indeed cause weird effects (it also would with EXR then, of course). Generally AE should handle a single Object ID an Z depth channel fine, though, if you realyl didn't exceed the file format specs.