FFVI: Divergent Paths

Insert a subroutine at the start of the scenario split code, right before the screen fade but after Mog is spawned as an object.
Add an action queue that pauses event execution until completion.

In this action queue, make actor $0A do the following (Mog is still actor $0A, yes?)

> Set movement speed to normal
> Set layering priority to 0
> Set to walk while moving
> Set action to $00
> Set to face down

Code:

{0A-87}               Begin action queue for character $0A (Actor in slot 10), 7 bytes long (Wait until complete)
{C2}                  Set event speed to normal
{C8-00}               Set object layering priority to 0, (low nibble 0)
{C6}                  Set entity to walk when moving
{00}                  Do graphical action $00
{CE}                  Turn object downward
{FF}                  End queue

That should at least clean up the animation trouble whenever the scenarios pop up.  The other place it happened was on the airship... not sure what you could do there.

EDIT: You didn't mess with ram addresses $09F8 or $0A11 did you?  Those could mess with Mog's field display, the latter especially for his lower body.