Don't worry, those last coordinates shown are normal. These are saved in that .isd file inside the "Civa" folder, like all previous states of the device.
The "autofill" seems to arise if you enter the coordinates in the wrong format, because FSX often doesn't show a "0" (zero) where you have to enter one in the CDU.
So please check your inputs again or give me screenshot with the FSX coordinates and your input on the Civa and I might tell you what was entered wrong in that special case.  :)
Maybe this helps too. http://forum.avsim.net/topic/326447-civa-ins-issue/page__view__findpost__p__1925566