As far as I can tell, my problems have been caused by me renaming the automatic import projects in Aperture. I did notice that Aperture kept creating new empty projects for the same month.
This solution from Jannem1970, posted on this thread https://discussions.apple.com/thread/3585677?start=0&tstart=0, seems to have done the trick for me.
- turn off automatic import for Photo Stream;
- identify 'the ghost'-projectfolders, select and delete them;
- close Aperture (this saves the current setting and condition of your library);
- open Aperture again;
- turn on automatic import for Photo Stream.