I have a vague recollection of the sort order for sections not matching the sort order for the fetched results controller causing issues with the section handling. There might be another thread about just this issue. So check to see if the sort order matches the section order and if not, please try correcting that.
If that doesn’t work and you are using any custom code, please post your code somewhere online and provide a link and I’ll take a look.
Take a look at this thread to see the change I’m talking about (though I’m not absolutely sure if that is the same issue you’re seeing):