Thanks folks for the input, much appreciated. I've been having another go this morning and the left hand side goes in an absolute treat, but the right hand one will go in one turn relatively easily and then bind completely. I've tried the other cup in there gently to see if the've accidentally put in a clockwise thread, but no joy with that.
The bottom bracket shell is strongly bonded in to a Bamboo Frame in much the same way that a Carbon Fibre framed one is. So once it's it there's no way to remove it, which is why I'm keen for it to be correct from the start. I've actually pushed it as far as possible to the extent that I needed to clamp the BB removal tool in the vice and use a lot of force on the shell to remove the cup.
I've eliminated the dirty threads problem by using a brand new bottom bracket and the shell from the bike is brand new as well. I've had a good look at the shell threads and there's no swarf in there, it's actually really well machined with no visible problems or burrs, it just doesn't work!
As
@Gary E has said because these are all small run items they must be all from the same batch. However I would expect that there must be more of them out there in the wild so maybe someone else is having the same issues.
There's a really good old school bike shop not far from here who've helped in the past, maybe I'll swing by shortly and see what they say. One issue is that you can't clamp the shell into a bench vice to work on it, because you risk deforming it.