I’d originally put the reversed one on MIDI in, I think - I’d need to check my build pictures. Yes - I did - but I swapped it over to out before testing because of a picture in the wiki. Argh.
There was nothing in the wiki about the connectors being different, and when I looked at the pictures they were inconsistent as well, so figured the logical ‘difference’ might be that the one for out was different in some way - there’s probably some documentation that makes it clear in the repository, but I was looking at Wiki/build guides when assembling.
V4 viewed from ‘inside’ - MIDI out is different.
V4.1 viewed from ‘inside’ - MIDI out is different.
V4.1 viewed across - all three match.
The MIDI test played back fine when first assembled, but that was before I hooked up a controller - when hooked up, it initially didn’t show any activity on the MIDI in… so I then looked more closely at it and checked the V4.1 and V4 guides and realised that there may be a problem - but at that stage, I think the damage was done.
With the Zynaptik board disconnected, the Zynthian runs fine playing the MIDI Test with MIDI channels I’ve assigned so I have to assume that the reversed MIDI in wires fried the board (as I only swapped them over to other ports after seeing the odd behaviour, like the MIDI LED being on the instant I plugged a device into the out port.
I like the MIDI activity LEDs and have no problem at all with how it’s implemented! Just frustrated that I had to wait four more days for the kit because of UPS (I’ve never had a perfect delivery from them - I must have upset the gods of UPS once), then have a component I didn’t realise wasn’t right which wiped out a chunk of the Zynthian-ness of it.
I haven’t soldered anything more complex than a car wiring loom in 5 years, eyesight’s too messed up to focus and no depth perception so I tend to miss my target… 
I would very much appreciate a correct MIDI socket and a working board! Apart from this it’s gone together exactly as it should - from assembly to SD-card build to playing a multi-instrument setup from the Keystep Pro.