On login no desktop background, new icons, new theme, and keyboard shortcuts not working?

Today I logged into my desktop to find that my theme had changed from the default to the blue and green 'no desktop background', the icons were different, there was a new trash and computer icon on the desktop, and the shortcut for terminal was not working - these should all be set to the default on this new install as I have not changed any of this. I am concerned over what else might have changed, and how?

I have now used Timeshift to roll back to the very first snapshot (for some reason the more recent snapshots did not resolve this issue) but if something I have been doing caused this please let me know so I can avoid it in the future:

  • Configure the swap file Install Ubuntu MATE 20.04.01 (minimal install option) using Ubuntu 20.04 with btrfs-luks full disk encryption including /boot and auto-apt snapshots with Timeshift, configuring just the swap file option twice the size of RAM, rather than swap partition, and stop after completing Step 6.

  • for resuming from hibernation: calculate resume_offset, and use it with the swap subvolume UUID from fstab to edit GRUB_CMDLINE_LINUX_DEFAULT= in /etc/default/grub. sudo update-grub and reboot.

  • Return to the install guide and complete Step 7 to configure timeshift, timeshift-autosnap-apt, and grub-btrfs.

  • Fix issues with lockscreen not appearing on suspend resume with: dconf reset -f /org/gnome/desktop/screensaver /org/mate/screensaver /org/mate/power-manager

  • sudo apt install deja-dup and so Deja-dup can use my Google Drive authenticate it with: sudo apt install gnome-control-center gnome-online-accounts and XDG_CURRENT_DESKTOP=GNOME gnome-control-center.

  • Create deja-dup backup.

  • Install Insync but do not sync anything.