Not sure I understand the question... MHF heads ("Mark's Head Format") are standard heads/skins created by Mojang which players can use in their own game. The idea is to provide a head which will never change. See here for a full overview.
I wasn't aware that this happened on EMC... You can always try to place these in your /vault, close it, and take it out again to see if that might change things. If that still doesn't change try contacting Senior Staff directly.
Happened when we switched to 1.8 I believe. Aikar added a change that auto renamed them I believe. Haven't seen one of these names for along time personally.