I solved this by editing the plugin files. Not ideal, but when the plugin author ignores your emails and forum posts it’s what I had to do (I have paid for the pro version…).
In the rare case that this may help someone else, in UserInsert.php I added the filter
$userData = apply_filters('user_meta_pre_user_register', $userData);
before
$this->userData = $userData;
$this->setMetaData();
as I realised that when the data was being sent to setMetaData() it was too soon and hadn’t reached the filter so didn’t have the extra meta fields added.
Why this is happening in this plugin, I have no idea….
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