Have you tried another computer. ? Maybe your programs are seeing a shadow copy of garmindevice.xml somewhere else in computer ?
Do you have any virtual drives in that computer ?
Is your Garmindevice.xml being updated at boot time ? (completely power off device,switch on let it reboot and then connect to computer see date and time of garmindevice.xml)
Have you tried flashing firmware ? previous version ? Same version using updater.exe ?