For years I have been working with M100 & AE without any issues. Just last week, I exported a clip out of M100 into AE, created my effect & imported back into M100. I saw a very, very slight luminance or chroma change (it is so slight, I'm not certain which it is) from the original M100 file to the AE file.
Nonetheless the change can be seen.
I am using m100 suite 1.1 in 10.5 and ae cs4. I am using m100i codec in an sd project. I of course exported the ae file as an m100i file.
Can you maybe post the file somewhere? I guess there haven´t been changes to the Media 100 i codec itself in quite some time, but maybe something changed in the Apple MJPEG B codec, which is the base for the Media 100 i codec? Or your original file contains illegal RGB values in its YCrCb native file, which cannot be preserved by a YCrCb->RGB->YCrCb conversion.