See P1968 for log. CN message groups alone about two hours to index, which is more than all other message groups across all sites.
There seems to be something blocking there, because even though I ran with 4 threads, only one of them seemed to be doing something at a time during CN groups. You can see this in the log by having bunch of groups complete (not shown in the log) at the same time, and new threads spawned for new groups at the same time (shown in the log).