Burning Crusade has spread this phenomenon to other bosses, too. In Karazhan alone, the Prince, the Maiden of Virtue, and Nielas Aran seemingly cast whatever it is they cast more frequently. Infernals, Holy Fire, Flame Wreath, the whole shebang. In general, this crops up for encounters that have an element of randomness. Malchezar's infernals can drop wherever they'd like. Safe spots are only safe until the randomness of the encounter decides to be random. In the case of Deep Breath, it simply occurs for your raid more often because you didn't take the proper steps to prevent it.
I actually think it's sort of fun to see so many people complain about these things with every patch because it's a good sign of the encounters actually working as intended. I just wonder how many encounters this has applied to over the years. Onyxia is most famous for it, but how far does Deep Breath Syndrome reach?