Right now I've got Sonarr or Radarr pulling down nzb files to a watch directory, and newsbin is picking them up to download.
That's not really how it's intended to work. I'm kind of surprised it works to be honest. Instead the intent was to add a downloader in the download clients section of Sonarr (Newbin pretends to be SAB so use SABNZb). Then in the remote NZB options in Newsbin, you set the port and just the APIKey. Make sure the same API key is in sonarr.
Then the NZB's get fed directly to Newsbin over a connection and Sonarr can monitor the downloads.
So about your issue, you don't see any error in the logging tab in Newsbin? You could send some of the problem NZB's to "ts @ newsbin.com" and I could try downloading them.
This sounds like an unrar problem and not a sonarr problem.
I wouldn't change your setup at this point. It'll just add more potential issue.
If I can try the NZB's I might be able to tell you something.