There are two parts to ID prefernces that you should be backing up, and most times you should replace both. There's a good chance, if this is happening a lot, that you haven't really cured the problem because you only did half the job. Please see Replace Your Preferences
Even the Adobe Engineers don't seem to have a real handle on why prefs get corrupt (and there are probably many reasons) because they don't seem to have a method at the moment of collecting the data. Force quitting prevents ID from writing the prefs files on close, so there's a good chance that's a contributing factor here, but it may be that you find you have to force quit because the prefs are already corrupt in some way, so it's not an absolute.
Do you have any third party plugins?
So you think there is no other way than what im doing, which is when they revert back to the default
I just place back the Adobe Indesign folder and re-start indesign?
Did you read the link? I give directions for backing up a GOOD set of customizations so you don't have to start over each time.
I think Harbs also has a prefs manager availble at In-Tools.com that can do that for you, as will Blatner Tools from dtptools.com, I think.