I think there is a problem that only comes up on initial sync.
I have newssync configured to split disimilar topics and to NOT merge similar topics.
On all 3 times I have installed it, I have gotten what I call a "superthread" where a very large number of messages with all manner of topics collect. See example here: http://www.battime.com/forum/viewtopic.php?t=178
As you can see, these threads have nothing in common, yet they were grouped together. I also believe this only happens on initial sync, because once I delete the thread, I have not seen another like it recreated.
Anyway, other than that, the only other problem that I have is that I am unable to run go-newssync or newssync.php from the command line, all I get is a bunch of errors, but I think that is related to the way php is installed at my host. Instead I run it via a wget command that is set on a cron job.