For the same reason people in places where it snows every year still remember the really big blizzards: some floods are worse than others. Any given generation will have a flood they recall that set the (ahem) high water mark for comparison to future floods.
I don't know, if I know it floods every year, and there is a really big flood, I don't think I would act like the flood was something completely out of the blue. I would probably mention how it was much bigger than the normal floods.
For that reason, I think an event completely different from the yearly flooding is more likely, for example the Minoan eruption or Black Sea deluge hypothesis.
