After a while ive found these 2 mods that affect the stones of barenziah and i believe have affected the "no stones unturned" quest.

Non quest location for Stones of Barenziah : http://www.nexusmods.com/skyrim/mods/33530/?

Freedom of Speech : http://www.darkcreations.org/forums/files/file/402-freedom-of-speech/

They both affect the location of the stones and i didnt know that.

Now can i remove 1 without it messing my ongoing savegame up?

I prefer to keep freedom of speech.

But anyways thanks in advance to any who try to help me.

Unless you create your own patch you're kinda screwed.