Is this a file you are converting to the new version? ID always treats the first save of an existing file iin a newer version as a new document with Save As, to protect you from overwriting the old version. This should revert to a regular save on subsequent times.
If you always get a Save As dialog, there's a problem, eihter wih permissions someplace or a conflict with other software, or perhaps just corrupt prefs. See Replace Your Preferences