So you're saying that you use one client to download headers within your server's retention and make NZBs from them, then load these NZBs into Alt.Binz and try to download (from the same server), but no joy? That, needless to say, shouldn't be happening. Any error messages in your Log? Also, posting a sample NZB somewhere could be useful.
(This is assuming that it's not the Giganews issue with DMCA'd posts, with one part missing per article)