Okay, it's "fixed" by an ugly method that has a major problem, but at least it all works through scribe. The problem is that if someone directly calls the init.d script to restart syslog-ng, it will cause the same problem as before, the files will be all messed up.
As long as syslog-ng is restarted only by scribe, it will be okay. That may be all I can do for the night. Something is happening, this is were I could really use one of the problem routers to test, I need to put a bunch of flags in the code and see where it all goes astray.