I'm officially stumped

everything looks right. just not meant to be on your device I guess.
I'm reaching here.. but maybe there's some issue if you used MTP? Versus using ADB push to put the image on your phone?
Have you noticed if the modem or boot image has updated (those would be fast flashes) and just system is not working? or all 3 not working? You'd have to check the software settings under About Phone to see if baseband(modem) or kernel changed.
you could always use the dd command to try and flash the image while in TWRP..
Code:
adb shell
dd if=/dev/zero of=/dev/block/platform/msm_sdcc.1/by-name/system
dd if=/sdcard/flash2/system.img of=/dev/block/platform/msm_sdcc.1/by-name/system
The 2 dd commands should take a minute or three to complete.
Or just wait for engine95's stock rooted ZV6 rom.