I put the command
/summon Zombie ~ ~5 ~ {Equipment:[{},{id:"minecraft:chainmail_helmet"}]}
into a command block, and it gives me a zombie with diamond boots. I tried this with all other armor types and it always gives me a zombie with diamond boots. If I remove the {} in the beginning of the equipment tag, nothing works. If I were to put anything besides boots AND boots on, it shows a zombie with pants and boots. If I put another on (that isn't already on) It shows a zombie with a chestplate, boots, and pants. Also, If I JUST put a helmet on, the zombie still burns, and the boots (the helmet) act like boots.
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Like Anon Ymus said, the order of the equipment slots is important. Use this:
/summon Zombie ~ ~5 ~ {Equipment:[{},{},{},{},{id:"minecraft:chainmail_helmet"}]}
Read on here http://minecraft.gamepedia.com/Chunk_format#Entity_Format for the format
Unable to reproduce. You are also trying to put a helmet in the boots slot, which might be your problem. Also remember the array should have length 5, so add three extra empty compound tags.