Cheddar, the kind of cheese allegedly at issue in this outbreak, appears to be a low-heat cheese, so you wouldn't start by heating the milk to pasteurization temps. If the milk isn't already pasteurized, the resulting cheese might be contaminated.
European soft cheese makers allegedly follow protocols to ensure that there's not substantial bacterial contamination in the beginning; they carefully handle the milk through the beginning of the cheesemaking process, after which the culture and salt and acidification stall any further bacterial growth; then aging cuts down any bacterial population to safe levels, and it's never reached a level where it could produce dangerous levels of toxins.
Competent American raw-cheese makers would do the same thing, but in the interest of supplying "raw milk product" fanatics, unscrupulous businesses will cut corners for profit. High contamination levels of the initial raw milk, or substantial cross-contamination after aging, is probably what led to this and the company's previous cheese contamination problems.