Premultiplication issue with two jpeg sequences
Part of it may be the fact you are using JPEG sequences.  JPEG isn't a pixel accurate format and you are going to have some differences in block quantization that could potentially result in mismatches.

I don't think that is the only issue since it is a bit too regular for it to be the only issue, but I'd try to use an intermediate format that is a bit more lossless for doing things that need to be pixel accurate match up.