I haven't run into that exact problem but something similar. I would try R-Clicking on the clips and going to Item Properties > Format... and make sure the Alpha and Composit is the same for both clips.
If the Alpha Channels settings fro both are the same, the next step I'd try, is to make both clips the exact same codec. And just for the sake of experiment, export both into another Codec, e.g. Animation or Uncompressed10-Bit, and see, if it still happening then.