This is a "new" problem with Acrobat
I have recently been having the same problem with some PDFs not allowed to be saved after changes from Acrobat Pro (not Reader). This has been saving as it should until very recently, and I have no idea what changed. Must be a background update from something, but I don't believe its from Acrobat itself, as I seem to remember it working well after the update to v10.1.4 and "broke" sometime later.
Not sure if that helps, but its one more data point to be considered...