Just finally found a solution for this so thought I'd post it here as a question and answer so I find it next time I google it:
I have a .launch file which I can run by context menu (Run As...), but it is not being added to the list of Debug or Run configurations like it should. Why not?
There is something wrong with the launch config. Possibly a project is being referenced which is closed (that's what it was for me)...
So the launch may work (in my case this was because the project wasn't actually required) but any issues like this will cause it not to be added to the list of launches. To figure out what the cause is, you can "Edit <launch name>..." from the Debug view...this properties window will show you any errors. Once those are fixed, it will add the launch to the list of run configs.