This has been bugging me for a while, but my crafted totems like "Totem of the Sabertooth" will randomly just stop consuming with autoconsume on. This started back when AoD was released. They will still say they are autoconsuming when you right click them, but I have to disable autoconsume and reenable it to get them to start autoconsuming again. I think it has something to do with zoning because this behaviour never happens when I turn them on and stay in the same zone for extended periods of time.
after I read this I checked my compact sumac harvesting kit and it was acting the same way. Edit: spelling
One condistion where totems stop auto consuming is when you are mentored to chrono below the totems level requirement, it will reset the auto flag to off. Zoning at the same moment as the auto consuming is suppose to take place could also clear the flag, but is a bit more unlikely unless you're a slow but often zoner.