So, there isn’t really line numbers in obfuscated bytecode, I’m guessing you mean after that first big loop that sets the first local variable? In function afe/a (net/minecraft/item/crafting/CraftingManager/func_82787_a/net/minecraft/item/crafting/CraftingManager/findMatchingRecipe)?
So ‘why’ is it that GT6 tools cause that to be processed but vanilla tools don’t?
You literally replied to the reason for this on IRC a while ago with a comment on how horrendously broken this chain is, so guess what, I already fixed that part. 
But still, as detailed above, just add a check for if the entire grid is empty with an early out, and everything should work.
I posted that a lot further back then a minute ago, lol.
So I added asm for that, latest secret download, here’s the template message about it if you want to try it @theJ89:
This Version should probably be working for you. ^^
(note 1: The scary sounding Description is only there to make sure people don’t use that Version lightly.)
(note 2: if you use this Version more often, make sure your Browser didn’t cache the Download)
On a plus side too, it will also make other empty recipe lookups a lot faster as well in mods, lol. I wonder if AE2 will benefit in some way…
Note, one of the Fixes I made earlier technically fixed this Issue on a different End, so what OvermindDL1 did was effectively nothing in that regard, since i fixed it at another point already.
However when I tested the ASM thing (undoing my fix in order to test it ofcourse), I noticed that it did absolutely nothing, so it needs to still be worked on, but when it finally works, it will reduce Lag on many other points! 
Confirmed fixed in latest snapshot! Awesome work. Thank you both! 