Sorry I forgot to reply earlier. A couple of the repos in the project on one of the grok systems appeared to be damaged though the indexer didn't indicate that in the logs. I updated the hg package, and removed all the repos in the nv-g11n project along with all the indices/caches/xref and restarted the indexer.
This should fix the stale bits you were seeing, but keep an eye on it and let us know if you notice it creep out of date again and I'll look into writing some sort of script that will check the repos once a day just to make sure the local opengrok repos are current and undamaged. e.