My guess is the following (at least this is how the problem arised with my installations):
As a cautious guy, you first installed CS3, tested if everything is OK and then uninstalled CS2.

Uninstall takes away the file associations, regardless if there still is an other (newer) version of InDesign installed. And Adobe does not provide a hack for the registry as in the early days of Photoshop (I suppose the problems with such a hack are much more important than the solutions it provides).

The only way, I know about, to restore the associations and icons correctly is to reinstall the (CS3) software.

Lucien.