This behavior is correct since a Reader-enabled PDF's has not the right to use the setDataObjectContents() function.
When you open an attachment out of your PDF in Reader then its path isn't the temp directory or so but a path pointing into the PDF.
This path may look like:
Without the rights for setDataObjectContents() you cannot save the attachment into this path even it has Reader Extensions.
So, you always have to save the attachment to the hard drive first.
Acrobat has no problem because it has the setDataObjectContents() right, but Reader doesn't.
Reader only could to this when the form has enabled by LiveCycle Reader Extensions Server, but you'll need many $$$$$$ to own such server.
So, the workaround is to save the attachment to the hard drive first, before you open, edit or save it with Reader.