Yeah. Last time I tried to manually upgrade IC2 to the latest 1.2.5 version in my Tekkit client, I had the same problem with recipes not working with NEI 1.2.2.4. But when I tried to update NEI, it broke some other things. So its a lose lose.
I use PEX + NoItem for banning items.
You can use NoItem with GroupManager, but instead of doing:
-noitem.(nocraft|nopickup).226
you would have to:
-noitem.nocraft.226
-noitem.nopickup.226
which makes your permissions file a lot more complicated.