Molly, I believe the MKV version is not a re-encoding but the mpeg stream repackaged in an MKV container.
I just got to looking at the test4-analoclean+magicup2 version and don't like it as well as the first version. The original preserved some grain and looks more natural with less digital artifacts.
How do those versions relate to the ones tagged as deghost? Is that just the analoclean+magicup and analoclean+magicup2 again or something new?