I did not change mpeg options, though I wasn't sure whether they would apply since this is an m4a or aac file, not mp3. But for mpeg, ape was not checked.
What I did: m4a files had previously been adjusted with aacgain (variant of mp3gain).
In mp3tag, I then right clicked the file, chose tags, selected the itunnorm tag, clicked the red x, clicked ok.
After that, when I ran aacgain, it did not recognize that the file had already been adjusted. You can tell this because it doesn't list a volume for the file. You can re-analyze and readjust, and since the adjustment was already made, the new adjustment will be zero. However, because the old tag was lost, you could not undo the original adjustment.
When I looked at the tag with an editor, I also saw that replaygain fields had been reordered by mp3tag.