It's normal that it's all read only, in Reader when you open a form that has broken rights it automatically makes everything read only. When you open it in Designer it converts the PDF to an XDP so that's why it's no longer read only, it's also why opening it in Designer will strip the rights if save the PDF from there.
Now, are you sure it's saving the PDF that breaks the rights? In my experiance it's usually some script that changes the template that breaks it, but it appears like it's the save that does it until you dig deaper. For example, if you change the SQL query of the data connection and then save it will break because the template has been changed. You'd actually have to reset the properties you changed back to the original ones before saving.
Anyways, it's hard to tell you what could be doing it without going through the script on your form, but focusing on that would be my advice.
Chris
Adobe Enterprise Developer Support