Common problem on the 1117 firmware. Roll it back to an older official firmware and your problem should go away.
^This. But, it seems like you have already have tried flashing the older firmware.
name: Antminer-S9-all-201704270135-autofreq-user-Update2UBI-NF.tar.gz
sha-1: 0515029015ad8dcedb185367fc5f829851dc65ed
With latest firmware Fri Nov 17 17:57:49 CST 2017 I do Not see a Hardware Version and BMminer version and zero hashing on any of the boards
When I load up firmware version from April 2017 I see 2 boards and they hash but not on antpool only on nicehash.
It sounds like at least the other 2 boards should work now. Try unplugging the faulty board and see if the miner will hash natively using the other two.