Now I am puzzled.

I did a clean install of the forums (imported the original DB that had no posts, etc. into a new DB) and imported the rec.sport.unicycling newsgroup and now I only have 15 messages in the usenet_article table and when I look at it, there are reasons that I see that they were not inserted. Stuff like "Re(2):" or "Re: [Re:" are in the subject and some of those have no refs (so the orphan replies code doesn't associate a ref for it). Earlier today, I had 52 messages in the usenet_article table and most looked like they shouldn't have had the problems. I also downloaded the latest zip of the hack and replaced the newnews.pl script with the one I had (which was version 2.3, but from before the addslashes() fix was put into the code replacements which I didn't think affected the newnews.pl file). Another thing I did was set it for just the one newsgroup without using the multiple servers since you mentioned the bug with that (although I never saw that particular bug, and you deleted it from your post). So, now it appears to work. Thanks for looking into this problem and sorry about trouble.
Anyways, I think a feature that would be nice to help with posts not being inserted would be to have a feature in the control panel where the posts that are still in the usenet_article table are listed and then have an option to choose a thread to put it into. This would help with the posts that have weird subject lines since one unrecognized post makes all the child posts get stuck as well.