Thank you, I got it.
The problem is that not all the EXR files in your sequence have the same channels. If you import each frame individually you'll find that EXtractoR works as expected, but it'll show different channels in the list. You can also see this by clicking different frames in the project window and checking the readout indicating the number of channels.
The reason this causes a problem has to do with the AE API. While I'm retrieving channels by their names, the API internally uses an index number. For a sequence it uses the first frame to index the channels, but if a later frame has different channels the index will get misaligned and you'll get the wrong one.
Hopefully this happened because you made changes to your channels and didn't re-render the ealier frames, not some Blender behavior.