The sequencer generates automatically material instances ("_animated") which breaks the link to the original assigned material instance. The only "solution" is to re-assign your material instance afterwards again to your mesh. I'm also trying to make a blueprint which auto-assigns the material via construction script but this also does not work well.
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UE 5.1: Problems (and only half-solutions) when animating Material Instance Parameter via Sequencer | NatokHD