Many places use canned nacho cheese, it's pretty much the standard for cheap nachos. I thought the article was referring to canned at a factory vs fresh block cheeses.
Could have been a bad batch from the manufacturer, or, it could have been poor handling of the product.
Remember McGee's takedown of Ruhlman's habit of keeping a pot of stock out at room temp and heating it up every day or so? Botulism was cited as being able to grow at the bottom of the pot as it was fairly deep. A slow cooker type setup with melted cheese in it could also foster botulism if it weren't maintained safely. (like if the pot was repeatedly left out after closing, but the heat was turned off for 6 hours -or if it wasn't cooled down properly prior to refrigerating) Too much time in the danger zone with a deep pool of undisturbed cheese providing lots of food (protein, sugars, water) will breed botulism. Even if a product is full of stabilizers, preservatives, texture enhancers, etc. doesn't mean people can ignore proper storage and handling techniques.
And now, people are going to pile on here saying that it's 'oh so unlikely', 'stop scaring people unnecessarily'..... Nine people have been sickened, some may be permanently disabled. Botulism can be cultured relatively easily. Safe food handling techniques can save lives.