Looks like we actually found some info on this after doing some more digging. Apparently WP by default only shows 30 items in the custom field drop down.

We had to add to our functions.php

function increase_postmeta_form_limit() {
	return 120;
}
add_filter('postmeta_form_limit', 'increase_postmeta_form_limit');

We set that number to 1000 as I have no idea why there would be a limit placed on this drop down. Whats the point of custom fields if you cant access them. So strange WP does this by default.

Anyhow, if anyone else has that issue hopefully this will be helpful.