If I have that many floodplains I always try to split them up among 2 or 3 cities. You won't be working them all for a long time, and that's some pretty serious unhealthiness.
As for how start tiles are generated, there's several steps:
remove bad features (jungle, ice)
remove bad terrain (tundra, desert, peaks)
try to add fresh water if needed
try to ensure at least 3 hills, adding them if possible
try to ensure at least 3 2F1H tiles, converting plains to grass-forests if possible
check for food (1 land or 2 seafood, generally)
Then, if the spot is not at least 80% as good as the best start, it does some more:
add forests (this bit is bugged, and adds forests to all possible non-resource tiles leading to the familiar buried-in-forests starts that BtS is famous for)
add resources until you reach the 80% threshold or 2*seafood + 3*land_resources >= 12 (note that because of the forest-spam bug, it's often impossible to add land resources; thus some over-forested starts are terrible, and some get tons of seafood because that's the only thing that can be added)
I'm not sure if floodplains are measured in the "goodness" measure, or if it's just resources. But I'd say in both your starts you just happened to have all the floodplains, and in the second one the seafood was probably added in the last step.
peace,
lilnev
