When you say edit the collection settings - do you mean the menu option Edit Kindle Collections or Customize? I think if the book isn't already on the Kindle and you send it, then there might be a gap. I'll put this on the list to test. Its a similar issue with the collections listed in the Device tab - once data is written out, its not read back into the cache in the same way as a new connect.
@CWatkinsNash - now you've gone and given both Kiwidude and me something more to look at

Well, without interesting suggestions there's no fun