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!
Easy mistake! At least you're not elbow deep in a car engine and wondering where the service manual got to! Ok, my first check would be the MD5 for the Media.zip after applying the xdelta, it should be: 8AB4E954A0F235F61FAD46CD2152D5B3.
I think we're going to have to do this piecemeal to find out what's wrong, or as a good friend of mine says: troubleshooting is a hard won skill!
Ok, that looks to be the same - this is one problem down!
Next step: might I suggest deleting the install (it won't delete your saves as these are stored down in ux0:data) and install the apk fresh off of VitaDB or from here. Then unzip Media.zip and install that into the game folder as instructed.
Stray thought: what plugins might you be using on your Vita? There are some combinations of plugins that the Unity engine simply won't play nice with, and I've no way of debugging or troubleshooting this so it's a problem that cannot be solved I'm afraid.
At this stage I've got no idea if any of those plugins could be causing issues. My best suggestion would be to ask around and see if someone can give you a copy of the vpk that's already had the media.zip put into it - we've tried everything else that I can think of, and if a known good vpk doesn't work then you'd need to address the plugins by turning them off one by one, but it shouldn't be nonpdrm or kubridge at least