AE Version: rev14.finale3
NEI Addons: 1.10.2.59
NEI Plugins: 1.1.0.6
Waila: 1.5.1a
Code Chicken Core: 0.9.0.8
NEI: 1.6.1.9

That's everything I have installed related to AE and NEI and shift-clicking in the pattern encoder doesn't seem to be working for me (it does nothing).

Is this on a server?
Do you have NEI Addons installed on the server?
I you don't you need to have the items in your inventory to work.

It is on a server, I thought neiaddons was entirely client side I'll try adding it to the server then.

That was the issue sorry about that, didn't know it had to be on the server as well.