GIMLI, I was JUST having a very similar issue too today. Mine is an ability that in theory morphs a unit into a Chaos-type version of itself. But for some reason, upon casting the ability, the "normal" unit doesn't change its tinting color (since I don't have models to match, I use the alternate unit looks the same but with a redder tinting), even though the rest of the Art applies normally: a few hand attachments, an 'Art - Caster' effect, etc.
Only when the transformation wears off, the unit changes its tinting color; and from then on every time they cast the ability, the reddened version becomes the normal unit while the untinted one has the Chaos-type damage and uses the PitLord sound set, etc.
Is this really due to some bug rooted in morph-based abilities themselves or is it something else? I'm using a custom version of Metamorphosis.
EDIT: Nevermind. Found the solution. Turns out that tinting is always messed up whenever a morphing ability is involved, even in non-custom units. Had to resort to triggers to produce the desired effect.