A stove certainly could produce more CO if it were starved of oxygen. On the other hand, if fuel consumption is relatively normal (or drops), and boil times extend, then probably what's happening is that one is just slowing the boil down. Of course, it would be nice to have a CO measuring device, but I wouldn't automatically assume more CO is being produced.
Interestingly, Trail Designs has come out with a device designed to slow down their 12-10 burner: a simmer ring that fits over the air inlets on the stoves. They were showing it at the recent GGG at Henry Coe State Park. I ran it. It had a long, slow burn, and baked a muffin in my Ti-Tri set up.
Adventures In Stoving