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!