More Info seeing as this also affected me and bothered me since I couldn't craft Blood Magic altar upgrades I took some time looking further into it.
Bug: SERVER SIDE BUG- Another thing to note the recipes SHOW that they work but you cannot actually pull the item out.
Known Partial Fix:
"With your script with the world (or savegame): the changes will be applied to only that game. The changes will also be sent to all connected players and as such this method should always be used on servers. Your script would be created in the /world/minetweaker/main.cfg file (in case of a dedicated server) or /saves/<savename>/minetweaker/main.cfg (for regular minecraft)." StanH -http://
www.minecraftforum.net/topic/1886008-minetweaker-add-and-remove-recipes-make-tweaks/
for more info minetweaker installation go to
http://minetweaker.powerofbytes.com/wiki/GettingStarted
With that said, the minetweaker config is strictly based off world so in turn you have to put the minetweaker in the worldsave folder, default name being "world", and that fixed a few of the broken recipes but there were still others. More on the issue I tinkered around with it for a bit further and found out that replacing a bunch of the .item.thermalexpansion.ingotenderium, the invar weapons, along with a bunch of other items named like that in the crafting boxes(under the minetweaksconfig for client/server) with their actual item ID fixed a portion of the broken recipes, none of which worked on Blood Magic. Only way I found to get Blood Magic working was to turn minetweaker config for Bloodmagic off on the client side because it is not launching in the server properly, and if you add it to the server its not launching properly.