First, please forgive my poor English, the following are from the Google translation.
If you don't understand, I really don't know how to do the.

BUG operational processes is:
Use stealth button all the material(not fuel) into the furnace, the result are not supported @name & @lore, But the default name items. If you use the mouse to drag and drop into it, it is supported.

My server info:
PaperSpigot-1.8.8
Plugins (8): PermissionsEx, WorldEdit, Vault, Essentials, OtherDrops, EssentialsSpawn, ASkyBlock, RecipeManager

thinks.

Can you provide the recipes you are using? Please use http://pastebin.com/ if you have a lot.

Does the same thing happen when running only RecipeManager?

I'm assuming "Use stealth button" was translated incorrectly and should be "shift click". Please let me know if that is incorrect.

It's "shift click",
This is my recipes

smelt SLIME_BALL
18:0
= 341
@name Glue
@lore It looks like the slime ball.

Thinks.

I am experiencing the same issue with furnace recipes. The only parameter which seems unaffected is the chance modifier. In the following recipe, 1% of the time a red mushroom with no metadata is created. Interestingly, the command flag does seem to be executed sometimes, but the behaviour is unpredictable.

SMELT roastedRedMushroom
red_mushroom % 30
= 1% red_mushroom
  @name &dRoasted Red Mushroom
  @enchant unbreaking 1
  @lore &f&oRed mushrooms... or brown ones?
  @command msg {player} Mushrooms, mushrooms! 

For what it's worth, the bug occurs in all instances when the player does not drag the item into the top slot of the furnace--hoppers do not work, and copying a furnace which has had the item dragged in with WorldEdit also does not work.

I've made some major changes to furnaces in the last couple days, which should help with the issues here and a few others that I found while testing. Just need to do some more testing to make sure I didn't break anything else before a release.