Open how and on what system? Mac? Windows? Do you use File / Open or do you double click on a document icon? Always use File / Open from the menu of the application first. Are you on Windows and does the document has the correct .indd extension?
In short: we need more info from you.
Can you please explain a bit more in details about your workflow about opening CS3 indd files in InDesign CS6. Then I might be able to help you better.