Thanks everyone for your help, I think I have resolve the issue. I measured the original link-pin that the builder put in at it was the same length as the pin on the missing link, but more central to the chain.
So, I took my Park Tool CT-5 and tweeked the missing link pin less than 1/8 of a turn to push it in, and hey presto! The link is still firmly seated around the pin, but the pin no longer catches.

I also noticed that the second smallest sprocket (which is mounted individually on the hub) is not completely true, so at some points it gets nearer the chain running on the smallest cog.
I'll strip it down again and check for anything that may have caused it not to seat properly.

Anyway, on a test stand at least the chain no longer jumps.