Not sure if this is a bug, but when your using shadows and not using Z-axis enemy movement. Peahat's shadow is 16 pixels beneath it at highest altitude. But with Z-axis enemy movement, Peahat's shadow is 8 pixels beneath it, "I think, I didn't measure it." However, when it lands it's shadow is normally placed. And is directly behind the Peahat. If you need more info our a text quest, let me know.
Here is what I have on.
Enable Shadows
Shadows Flicker
Enemies move through Z axis.
Not actually a bug - without Z-axis movement, shadow positions are "faked". For backwards compatability, the faked shadow positions will remain the same despite not corresponding to actual Z-axis shadow positions.
(In case you're wondering: the Peahat's and Keese's Z-axis flight heights are set up so that it makes sense that one can be hit by the sword from the ground, while the other can't, but can be dealt with by some midair slashing - and can be reached with the default Roc's Feather. The "faked" shadow positions aren't adequate at capturing this.)