If you boot with base norestore, you will see that indeed mtpaint is in the right click menu and that there is no xpaint icon. Likely your backup file restored both prior menu and icon.
While the menu is a single item and thus can be easily copied from /etc/skel, the xtdesk icons are individual and therefore the old (Xpaint both icon and lnk) must be manually removed after the backup restored them.
