Acrobat Will Not Allow Save?

I have Acrobat 9, Pro Extended (9.5.5). Running on Windows 7 Proffesional.
Also in case relevant, MS Office 2007. Autocad 2009Adobe Photoshop, Illustrator and Indesign CS4.
I create files mostly from programs such as Autocad, MS Word, MS Excel, or others and sometiems bind varisou PDF's into one document.
This all works fine, I can even work on the PDF right away and save.
BUT - Once saved and closed, if I open the same PDF again and make changes it will not let me save agina- I am forced to "save as".
Why? How do I fix thsi?
This is is getting really old and annpoying - it only started happening  in past month or two (I think).
Thanks in advance for any help!

Hi, thanks for replying.
I have tried that, but this "attribute", if you will, stays with the file once created - worse, even if I "save as", the same problem occurs with the newly named file after I close it and go to work on it again some other day. So I am now perpetually re-naming and deleting versiosn of the same pdf to work around this... losing my mind.
p.s. It doesn't happen when I am working with older files I have from other sources, or have created in past, or "saved as" - in past- only ones I create...
EDIT: it is happening to a file I recived from a consultant, thatI am marking up - I already had saved as "mark up..." but once i re-opened and later tried to save my notes/whatever, it would not let me.

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