I've heard of this one, and talked to people to try and resolve it, but none of them have ever come back to me and said "I got it sorted!" - it seems to be something that happens when converting the xdelta to Media.zip on Linux, despite the MD5 being the same. What I've told people in the past is to checkout the video by The TOKYO, have a look through the other discussions from people chasing how to get this going, and make sure you definitely do a clean install. Thing is: I've never managed to replicate it myself so can't say that I've got a definitive way of fixing it :/
Have a crack with the above suggestions and get back to me on this one, because I'd love to know if we do manage to nix it!
Hey my dude! See that shouldn't be causing any issues. Lets see about fixing this. The install instructions and video are here:
https://mrkane.itch.io/aperturereconstructed
And it's worth noting that the MD5 for Media.zip should be: 8AB4E954A0F235F61FAD46CD2152D5B3, so if we can get things to a known-good state by this step we've excluded a whole stack of problems already. Good luck, and don't be a stranger because I'll add a few notes to the guide when you do figure it out!