Well, this is an interesting find and I thought I'll share it with you.

I had a problem booting my Antminer R4 8.0 Th/s, batch 2, autotune-model.
So I went looking in here:
Bitmain.com: Three Ways to Restore Factory Settings (R4/S9/T9)
https://enforum.bitmain.com/bbs/topics/3957I used the last option in the list, IP Reporter button restore.
Usage: Please power off the miner, then hold down the IP Reporter and dont release it. At the same time, please power on the miner.
Releasing the IP Reporter after 5 seconds, the machine will automatically restore factory settings.
My miner restored with firmware Aug. 9 2016 and autotune settings were gone.
I am now suddenly able to control frequency and custom fan settings.

This was not my original problem, but I'm happy with it.
My original problem was that the miner jammed somehow in the booting process and didn't even show up in my router ip list.