I don’t have any kind of GUI open while I’m doing this. It’s really strange that the game is trying to update a crafting matrix I can’t even see. I tried looking up “activate” in the results as well and wasn’t getting any matches there either (I’m using the tool by holding the right mouse button while not pointing at a block, which may be why).
I think the snapshot has demystified the issue pretty considerably, though. What I think might be happening here, serverside each tick while holding one of the aforementioned affected GT6 tools with the RMB down, the code tries to find a use for it (e.g. blocking, debarking a log, emptying a burning box, changing the connectivity of a wire/pipe, etc), and then failing that it goes down a path that marks the tool as being updated (e.g. something setting an NBT value? I’m not entirely sure, I don’t have a whole lot of Minecraft modding experience.) which causes the server to send a packet to the client telling it that the inventory has been updated. Then, for whatever stupid reason, the client wrongly concludes that the crafting grid has changed and tries to find a recipe matching its new contents, and finds nothing because it’s empty (and because it’s empty and will therefore match nothing, it maximizes the amount of time it takes to scan for a matching recipe).
Edit:
Sorry about that! 
Didn’t mean to keep you or anything. I’m just a little indecisive when it comes to my writing, so I sometimes wind up rewriting things I write several times if I’m not satisfied with how it sounds the first few times around.