This issue could occur with child themes when the parent theme stores its options in theme mods.
In that case, edit the wpml-config.xml file provided by your parent theme, and change the line:
<keyname='theme_mods_parent_theme_name_example'>
to
<key name='theme_mods_child_theme_name_example'>
Then put this new wpml-config.xml file into your child theme’s directory, or in /wp-content/polylang/. You must create the directory if it does not exist.