I've got a modified version of the the high_poly eyes named high_poly4. When I load .mhm file with a toon that uses these eyes the eye material gets loaded twice, the first time with the right material, and the second time with an incorrect material. If I then select the same eyes in the eye chooser the correct material is loaded.
...
Selecting proxy file "C:/Users/Lindsay/Documents/makehuman/v1py3/data/eyes/high_poly4/high_poly4.mhclo" from eyes library.
Loading binary proxy C:/Users/Lindsay/Documents/makehuman/v1py3/data/eyes/high_poly4/high_poly4.mhpxy.
Loading proxy file: C:/Users/Lindsay/Documents/makehuman/v1py3/data/eyes/high_poly4/high_poly4.mhpxy.
Loading material from file C:/Users/Lindsay/Documents/makehuman/v1py3/data/eyes/high_poly4/high_poly4.mhmat
material fromFile final specularMapTexture C:/Users/Lindsay/Documents/makehuman/v1py3/data/eyes/high_poly4/EyeballSpecular.png
...
Compiling vertex bone weights for jammers3.obj
Loading material from file C:/Users/Lindsay/Documents/makehuman/v1py3/data/skins/wolgade-4k/wolgade-4k.mhmat
material fromFile final specularMapTexture None
Loading material from file E:/makehuman-builds/makehuman-20180305/makehuman/data/hair/short02/short02.mhmat
material fromFile final specularMapTexture None
Loading material from file E:/makehuman-builds/makehuman-20180305/makehuman/data/eyes/materials/brownlight.mhmat
material fromFile final specularMapTexture None
Finalizing MHM loading.
I haven't tested with the py2 MakeHuman because I only got the above output due to extra debugging output I added to the py3 version. I found this when trying to figure out why my specularMapTexture wasn't included in my exports.
I thought that it might have a duplicate uuid, but when I changed that I got a red error line in the logs about uuid not found in library. I removed the .mhpxy and .npz files but still got the same thing. So I changed the uuid back.
Reselecting the eyes in the eye chooser fixes the issue so I can continue to work.