The apiary and apiarist's chest is craftable but not in NEI. I think most recipes are there but for some reason get blown away. Also most of those are shaped crafting. Is there a trick to get NEI to update? If there is this would also fix the thermal expansion issues I'm having. The thaumcraft scripts called mods.thaumcraft.Research.refreshResearchRecipe a bunch of times but I think that may be a modtweaker/thaumcraft specific thing. The railcraft script imports NEI but never does anything with it. Maybe I'll try that.
Actually that probably won't work since the thermal expansion script imports NEI but it has similar issues with machine crafting.
UPDATE: I deleted the thermal expansion config and the machine crafting reappeared. I must have touched something I shouldn't have. Investigating with forestry now...
It's interesting that this is a fix considering the recipes show up in NEI if minetweaker isn't used.
It worked for thermal expansion but not the forestry recipes.
Thermal expansion was fixed by changing the reference to the steel gear from ore:gearGtAnySteel to ore:gearSteel. It has some other issues and I'm adding a few comments. I'll see about uploading it tonight. Hopefully someone will have some insight on the forestry stuff :p