How are you extracting the channels? And what format are you rendering too? (sorry I haven’t opened the project yet)
There’s a free AE plug in called extractor that will pull out each channel that is embedded in the rendered files.
It also could be that the format you have chosen doesn’t have the ability to render multiple channels within it. Pshop can, EXR can but jpg for instance cannot.
We have had issues where we don’t get a RGB channel if we don’t specify one in the multi pass and then other times we get those channels even though we haven’t specified.
If you have multipass checked and are ignoring the upper save area you should be getting either multiple files each with a channel extension or a single file with embedded channels that are not immediately viewable.