It doesn't look like you've uploaded the files properly, as the files that are missing don't exist in 2.1 -- they're 2.0 files only. The only way they'd come up here is if the hashes file itself hasn't been updated.
I may well be wrong, but I vaguely remember this happened to me. It was due to FTP preferences overwriting folders rather than merging. Theoretically I think you should get a prompt before any folder overwrites.