Turns out on the post-1999 Bongos, the speedo signal comes from the ABS system/front wheel via the transmission control module rather than from the speedo sensor on the back of the transfer box as with older Bongos.
Garage was convinced it was the transmission control module chip that was faulty: Ian at Bongo Fury managed to source one in Malaysia or somewhere (Mazda don't make the chip anymore

Fitted replacement chip, same problems still occurring. Garage are convinced it's still the chip: they think the replacement chip is duff as well.
Is this likely?
If hold light flashing is a common Bongo fault (is it?) then perhaps the Bongo we got the replacement chip from was scrapped because of the faulty chip. In which case sourcing another 2nd-hand one could have exactly the same problem.
Could something be zapping the chips? (we disconnected the split-charge relay system for the leisure battery just in case).
Not sure what to do: Garage wants me to hunt for another replacement chip.