Currently investigating. Was patch 0.6 your first version of the game or was it an older version? I think it might have to do with persistence from older versions.
Is your Archipelegates download from itch, version 26 (shows on download page)? The checksum should match if so. The patch will never work if the checksum fails. Even a single byte difference in the assembly file will result in a checksum fail typically. It's possible there is a compression/decompression thing going on that I can investigate, otherwise, there is no reason for the checksum to fail assuming we have the exact same download (I've downloaded it and tested many times on my end).