I actually just worked through this very problem today.
The issue is that you probably previously installed IJulia in your own ~/.julia package dir, and then ran ipython creating the julia profile (typically in ~/.config/ipython/profile_julia). The path to the kernel.jl file under ~/.julia was written into your ~/.config/ipython/profile_julia/ipython_config.py file (look for the c.KernelManager.kernel_cmd setting). You just need to update that setting to point it at your shared package installation, kill and restart ipython, and you'll be good to go.
