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I'm having (kind of) the same problem. If a hero/sovereign has leather boots on I can't buy and equip chain boots.
When I attempt to purchase chain boots, after researching them, I have the shopkeeper take my money and give me nothing in return.
Found the issue. chain boots dont show up correctly for Trog, Quendar and Urxen male units. It will be fixed in 0.914.
Bad luck for evil scumbags >) 
Sincerely
~ Kongdej
They could just use Boots of the Spider, though I can't think a good reason to do so. Maybe leather then?
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