Not 100% sure what exactly triggers this as this doesn't always happen but it seems to be a combination of a large "ingredient" list and fast changing of stored and crafting values.

refinedstorage-1.6.11

I've been seeing this too when crafting things with huge ingredient lists, any system with the crafting monitor just locks up the entire server, and without it it's like 5 TPS

to be honest, I get about 1 tick per second when I want to crafting something big and also tps starts to drop like mad with full discs once you hit about 20mil of different items in your storage, it starts to lose its purpose as one big storage unit and you have to make more, smaller ones and far away from each other, something needs to be done

I think this can be closed. I don't think it's an issue in recent versions anymore.