@myki,
I'm afraid I don't have any other bright ideas. I assume you're doing a 'safe disconnect' each time you disconnect the PC from calibre. The fact that most people don't have this persistent problem and you're having problems with 2 different Kobos would suggest maybe it's the usb cable or the usb port.
Incidentally, I installed the NightMode hack on my Aura6" at the same time as the Aura H2O, but then didn't use it much until yesterday, when I connected it to calibre - lo and behold - another malformed database. Some of these hacks definitely don't like me - so I know what persecution feels like