Steve,
I don't have any experience in this workflow but for the sake of trouble shooting can you take one of the problem Avid .mxf files and reveal the exact file for that with avid and then see if you could manually import that file into the AE project. At least that would tell you if AE can handle the file technically then it's some form of relinking voodoo going on, or whatever the proper AE term is for what Avid call relinkin. Are you dealing with group clips or multigroup clips in the avid timeline. If so perhaps commiting multicam before exporting the aaf might have an effect. These are just guesses on my part so take them with a grain of salt.
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