Since this is an InDesign question, I've moved it to the InDesign Forum for best results.
When you move to an new version of InDesign, it's stored in a newer file format.
Notice that your files opened from earlier files open with "[Converted]" in the title bar. That's why they won't overwrite your previous version. It's not a bad idea to carefully look at the files before renaming them to overwrite your previous version.
If you are opeing files from your previous version they are considered new files (notice the [Converted] appended to the name in the document title) and the first save will always be a save as to prevent you from accidentally overwriting the original. If you are smart you will give them a new name and keep the old versions intact. Things do go wrong.
In fact, I actually recommend you export your old files from the original versions as either .inx or .idml, depending on the version, and open that instead of the .indd in CS6. You're less likely to have a nasty surprise later.