As usual a few hours more digging has found a solution, I always like to share these with community so you can avoid making the same mistakes and getting stuck.
In one of my scenes (about midway through my game) I changed the fade scene effect to "fade over" or fade to new scene. It appears with this fade mode the character can be seen in its new position before the scene starts to fade.
I actually think this could be a bug, as I cleared my outfit update function and was still seeing this effect.
Simple fix was to set the fade effect back to "fade out and fade in", so it fades to black.. swaps the character, then fades in the next scene... sorted!