This is a limitation built into Reader by Adobe. Since Reader XI, Adobe allows the user to fill in and save an AcroForm (the type of forms created in Adobe Acrobat), but this does not apply to XFA forms (forms created in LiveCycle Designer). For these forms to be filled in saved in Reader, you need to apply extended Reader rights in Adobe Acrobat (or the corresponding LiveCycle server application). This cannot be done in Designer, so creating such a form is a two step process: Create the form in Designer, then open it in Acrobat and add the extended rights. From that point on, you can then fill and save the file in Reader.
By using PDFBox, you are adding another potential problem: I don't know how PDFBox will treat a reader enabled file, and if these extended rights will survive the modifications performed by PDFBox.
