I have not been able to associate the file extension with CS6 in Windows Vista. The .indd extension is already taken by another application, yet when I try to change it, it does not save.
This usually indicates something odd about the installation. Did you install another version after CS6, for example?
In theory you can probably edit the Regsitry, but it's probably easier to reinstall CS6.
While highly unlikely as the reason, Vista was not tested and is not supported for CS6.
What “other application” has the INDD association? Is it a different version of InDesign? Did you install the other version AFTER CS6?