In fact when you enable Generate HTML for all fields, your hidden field is
store at the end of your HTML and so the index of this field is not the first
one but the last one. That is why it is not working.
The solution
The multi-value field must be created before your set of html fields and it
works. Do not hide it in Notes. Just hide it with Type="Hidden" in the HTML
attributes of the field.
In fact when you enable Generate HTML for all fields, your hidden field is store at the end of your HTML and so the index of this field is not the first one but the last one. That is why it is not working.
The solution The multi-value field must be created before your set of html fields and it works. Do not hide it in Notes. Just hide it with Type="Hidden" in the HTML attributes of the field.