Same problem here. I have two iMacs side by side. 2009 and 2013, both using Sierra 10.12.3.
I have bought two copies, one for each computer. Comp 1 installed totally with no problem. Comp 2 installed basic X-plane app. When I attempt to update, it tries to load 6 Gb-compressed? (needs 25 Gb to match comp 1). Than I get a 'file changed detected, 1000 world terrain/textures10/loveg/sprs_cld_sdry_steep_d.dds . Choose overwrite file and click. Permissions error pops up and DOA.
This installation's folder is next to my XP 9 and XP 10 installation folders which function perfectly.
As I use IOS, Instructor and master, I have absolutely duplicate XP installations.
I copied the installer from comp1 to comp 2 and it ran the same errors.