If you can occasionally access your miner web interface it may be a network configuration issue than a hardware issue.
Is there any network conflict between you miners?
Have you tried changing you S3 miners IPs earlier or your all miners are at same IP?
Connect your pc to the same Ethernet Switch/Router your miners are connected and try accessing them.
You have another option to install the M's Antmonitor and do a scan.
If starts at good hashrate and further slows down leads to think about replacing thermal paste.

Yep! That's exactly how I had it and still nothing. Did a factory reset, re entered all the values and guess what? Works like a charm now! ASIC status on this one is all golden and hashing at an average of 460GH/S

Thank you so much for your help, you've been amazing. My first foray into some serious BTC mining hardware (I foiled with Block Erupters) and it was a little daunting. You gave me the help I needed

Now I just need to sort out this other stubborn unit!

Legend! I'll go have some dinner (the missus is on my back) then I'll attempt a repair on this other unit. Wish me luck!

Got my B4 S3's today.  Both of them have also the July 28 firmware ("Linux version 3.10.12 (xxl@ubuntu) (gcc version 4.6.4 (OpenWrt/Linaro GCC 4.6-2013.05 r38031) ) #140 Mon Jul 21 17:27:04 CST 2014").
Both of them run with very high fan speeds, much higher than the B1 units

3780 3960
4680 10560

The B1 units, at freq=225 run 1740 1620  and 1680 1500 rpm

The Bitmain support page does not mention this firmware.  Any clues why the high fan speed?

We can try to solve it if possible.
Tell me clearly the result of the below you already did.
Blade 1 -> Cable1 -> PORT1 in CP
Blade 2 -> Cable2 -> PORT2 in CP
You need to do this [1]
Blade 1 -> Cable1 -> PORT2 in CP
Blade 2 -> Cable2 -> PORT1 in CP
Further steps after the result of this. If possible attach images of Miner Status page before and after this mod.

If you are ordering a new unit they may send the replacement if its control panel with that.
For blade replacement I think they will only send if you are sending yours first.
If a return courier facility is there that should be utilized.
You should discuss with bitmain about various options if you are not able to fix this here.
As said earlier, time is money. So insists them to send first, you may give them some money as escrow for that.
Hope they will carry the shipping charge, I have no experience in sending for RMA.

I've now tried this...

Blade 1 -> Cable1 -> PORT2 in CP
Blade 2 -> Cable2 -> PORT1 in CP

The result is swapped, now Chain1 shows all dashes with one "o" and Chain2 is working fine. My guess is the blade is gone?

Good to see the results. So now, we found who is the culprit in the couple.
The Blade1 is damaged. And I'm almost sure that its the heat sink - thermal paste problem.
Connecting the damaged blade like this and running the miner may harm the chip in your damaged blade.
So, the option is to unplug the damaged blades power supply from PSU and the cable from control panel.
Then run the single blade or shut down the S3 completely to save your chips in the non-working blade.

Same time unscrew the small lengthy heatsink which is attached to the front side of the blade(Chips)
and check the condition of thermal paste application. If its not good clean it and apply some new thermal paste.
If its good contact bitmain and tell them you did all these thinks, may link this post. Bitmain will probably do RMA your miner.

Couple of points for those who might be interested...

Connecting the blades up to non-specific controllers...

Not easy to do. The blades are driven by a specific microcontroller (PIC of some sort) which is connected via USB to the AR9331. All of this is integrated onto the mainboard, and can't be removed. It also limits the number of blades you can connect to two, as the MCU in question doesn't have any connectors for more and likely lacks the resources to support them anyway.

As for the controller, it is already pretty much maxed out and would probably not be able to handle more even with the room to connect them. If you could get the MCU without the AR9331 board and also programmed with the appropriate firmware, you might be able to get it running on a generic PC or other more powerful host. You would however need access to the driver to compile it for a different architecture (not impossible, but difficult).

People having issues with controller boards...

Why not do as I do and post extracts from system logs here? Those who have worked with linux, and specifically OpenWRT might be able to help out, or at least give more specific diagnosis of issues...

Hey, I forgot to ask you some thing, which is your power supply and how you are connecting your miners.
Also tell how much load or miners connected to your Power supply.