Indeed there was a bug on Chrome and Opera that re-enabled Acceptable Ads during an update. And of course it is tempting to believe that this was intended, given the controversy around Acceptable Ads. But believe it or not, every release of every software has bugs. And consider the complexity of the code initializing Adblock Plus, migrating old settings, setting up default filter lists and dealing with different storage APIs for almost every browser. Also a single setting being reset during update, is not a case you easily notice during testing. So it is no surprise that a bug like that made it into the release at some point.

Beside that there are several cases where browser profiles can be corrupted. That includes browser crashes, bugs in the browser itself, unreliable storage devices and a few other cases. You will realize that users of every extension that can be configured, occasionally report that their settings had been reset. Of course that don't bothers you if you use the default settings anyway. But also there is not much extension developers can do against that.