NEI is not bugged. IC² machines are disabled, in favor of GregTech automatic ones. Look for "automatic whateverIC²machine"
If you really wish to use IC² machines for whatever reason you can re-enable them in the config and shapeless craft them from a GT one.
Although those are "inferior" as you wont have the ability to autooutput items and inability to use covers.
gregtech problems with textures directory maybe? As some people mentioned some posts ago.
Thanks SpwnX for the fast response, I kind of figured they were disabled for the GT versions, but want to make sure. As for the textures. I know the IC2 mod patch has a base dir of assets/. The base for for the GT patch is mod/, I tried placing it in the root of the texture pack as well as under the assets folder with no luck. I am also having issues with CC and Natura as well. I am using the Spahx PureBDCraft pack. I will shout on their forums again and try to get a response.