Set up all of your preferences with the program active but with no document open. When you're done setting everything as you like quit the program. When you relaunch the preferences should hold.
If it does not work the first time then try deleting your preferences first.
To do so:
For Macintosh Users: With InDesign closed Launch a Finder Window in column view and click on your home folder. With the Option Key pressed choose Library from the Finder Go Menu. Within the Library folder find the folder called Preferences and within it find the following two files and delete them: “Adobe InDesign” and “com.adobe.InDesign.plist”. When InDesign is next launched it will create new preference files and the program will be restored to its defaults.
After you set up your new preferences as I suggested above make a copy of your "pristine" preference file to use in the future to replace any corrupt versions you may need to delete.
For Windows Users: Hold down Ctrl + Alt + Shift when launching InDesign and respond affirmatively when asked if you want to reset.
Windows preference file: C:\Users\[User Name]\AppData\Roaming\Adobe\InDesign\Version [#].