I think the following should work:
In the Julia version that doesn’t show up, run
using Pkg
Pkg.add("IJulia")
Pkg.build("IJulia")
and then it should show up. You don’t have to add it if it’s already installed; it’s the build step that adds the kernel to jupyter.
I think you need to do this manually sometimes because Pkg thinks it only needs to build once per IJulia version (not per Julia install), but IJulia wants to be built per Julia install to be able to add the kernel.