I have BS animation checked, but none of that Z3 nonsense or anything.
What appears to be happening is:
In the Link Sprite setting box, the first screen of swimming sprites is labelled Floating, and the second screen is labelled Swimming.
ZC seems to take the swimming animation from the floating tiles, and ignore the swimming tiles completely; therefore no floating animation. I think I have pretty good proof of this in an example quest also if noone else can confirm it.