I started using phpmyfaq today and also run into this trouble.
There's a bug where the request token for the form submission gets reset.
I haven't been able to fix it, but I did manage to workaround it.
If you want to apply this temporary fix, edit file admin/configuration.php and change line 37 from
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if ('saveConfig' === $userAction && $currentToken === $csrfToken) {
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if ('saveConfig' === $userAction) {