Are you opening a file that was from a previous version for the first time? When you do that ID appends [Converted] to the file name and does a Save AS to prevent you from accidentally overwriting the old version, and because the file is considered a new file ID will default to the last forlder where you did a Save AS. Existing files that were saved already in the current version should always default to the folder from which they were opened, and if they are not I would say this is a problem with some other software that you are running. Do you have any third party lpugins installed for ID?
I'm glad that InDesign only *suggests* [Converted] being appended in the title tab, unlike that disagreeable habit in Illustrator of making you backspace the [Converted] out if you don't want it (or until you go to Illy prefs and turn it off).