Not sure if this applies to your situation. But we were having alpha issues where the footage was displaying the footage with an alpha, but the alpha channel looked nothing like the original in After Effects. After Interpret footage tweaks, plus trying ProRes 4444 and Lossless with Alpha and getting the same result, I saw this tip: Apple ProRes Graphics 4444 Alpha in Premiere In Premiere, right click on your Sequence and go to Sequence settings, then Uncheck the "Composite in Linear Color".
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