I was also having this issue as the updated plugin crippled my staff directory customization I had made.
I found a temporary workaround.
If you edit:
/wp-content/plugins/staff-directory/classes/staff_directory_shortcode.php
Line 290 and 291 and add the shortcode values you want to the arrays.
i.e.
$accepted_single_tags = array(“[name]”, “[photo_url]”, “[bio]”, “[category]”, “[phone_number]”, “[email]”);
$replace_single_values = array($staff_name, $photo_url, $staff_bio, $staff_category, $staff_phone_number, $staff_email);
I added E-Mail and Phone Number.
This will only work for the variable listed between lines 276 to 281. If you want different variables I would suggest adding more lines after 281.
i.e. for extension
$staff_extension = get_post_meta(get_the_ID(), ‘extension’, true);
That should let you add [extension] and $staff_extension to the array in 290/291
Of course these will break if you upgrade the plugin.