After more playing around, I now have a workaround whereby using a Mini DisplayPort to VGA adapter instead of one of the Mini DisplayPort to DVI adapters, i.e. an analogue connection to one of the displays instead of digital, seems to work and allows me to have 3 active displays configured like so:
Display 1 connected via HDMI to DVI adapter (into HDMI port)
Display 2 connected via (passive) Mini DisplayPort to DVI adapter into
Thunderbolt port 5 (as in the diagram in the above article)
Display 3 connected via Mini DisplayPort to VGA adapter into
Thunderbolt port 2.
However, I was hoping to have an all-digital solution as the above Apple article suggests I can, so I'm still hoping someone will come up with a better idea!
UPDATE: This appears to be an issue introduced with OS X 10.9.3. Tried an identical machine running 10.9.2 and the second configuration I tried in the original question worked just fine. Hopefully it'll be fixed in 10.9.4, until then the workaround above is still valid.
Thunderbolt is not backwardly-compatible with any other display technology. It is an active technology, all before it were passive. It is a combination of video & PCIe.
You can connect Thunderbolt to DisplayPort, but not the other way round.
From how do I connect an Apple Thunderbolt display to a PC?
If the Wikipedia article is to be believed (and I do believe it is correct based on what thunderbolt is), then your configuration will not work.
Compatability
Apple Thunderbolt Displays, like the video input on Thunderbolt iMacs,
drop compatibility with all previous standards, including VGA, DVI,
and DisplayPort.[3] As such, they cannot be connected to computers
lacking a Thunderbolt port, including pre-2011 Macs and the vast
majority of PCs.
Thunderbolt is not the same as Display Port. Therefore you can only connect thunderbolt equipped Mac's (or some PC's with thunderbolt hardware and appropriate drivers) to the Thunderbolt display.
From the Apple Mini DisplayPort FAQ
- My computer has the same connector but the symbol is different, what does that mean?
Some Apple computer have a Thunderbolt port instead of a Mini
DisplayPort. Computers with a Thunderbolt port will have the following
symbol next a port although the port physically appears the same as a
Mini DisplayPort:
Thunderbolt ports:
Are compatible with all of the Mini DisplayPort adapters referenced
below in question 5 and with Apple Mini DisplayPort equipped displays.
Support adapters like Apple's Thunderbolt to Gigabit Ethernet Adapter
and Thunderbolt to FireWire Adapter which are not otherwise compatible
with Mini DisplayPorts. See Thunderbolt ports and displays: Frequently
asked questions (FAQ) for more information on Thunderbolt.
So with your adaptor you can drive a DisplayPort based monitor to your PC, but not a thunderbolt display as it lacks support for DisplayPort. That's why it didn't turn on and work.
Some Googling and I haven't yet been able to find a USB based thunderbolt adaptor, it seems there is talk of such a device using USB 3.0 to thunderbolt although at reduced speeds. There are a few thunderbolt PCIe cards available and some PC motherboards support thunderbolt.
Best Answer
I think this may be one of the few times that recommending reset of the SMC & NVRAM might be in order.
NVRAM stores display config, amongst other things - see The Eclectic Light Company - What is stored in NVRAM? (generally a knowledgeable resource)
SMC stores external video source in some Macs. I'm less certain this is going to be the useful step, but the same resource, The Eclectic Light Company mentions that treating them as a pair can be useful. SMC first, then NVRAM.
Persistence: EFI, SMC and NVRAM