Just for the record, I just got done with a 2 hour teleport session (been bouncing around 6 missions all using the same factions so I know the maps and map packs aren't the problem) and saw a faction other than CAF a grand total of once. I think it was vanilla independents. And again it was at a roadblock which is where I almost always see this.
When I say 99% of the time CAF spawns correctly that's probably not an exaggeration. I really believe though that something with roadblocks is up either with the mod or the way ALiVE is communicating with the mod but 1 time (1) over the last week or so I saw vanilla independents spawn in a city and I saw a roadblock nowhere near me. If it weren't for that I'd say it's only happening with roadblocks.
But as a whole, it's spawning 99% CAF insurgents. My missions have almost no fluff in them now so definitely leaning towards a bad config with the mystery hotfix posted on BIS.
Been meaning to try the "old" file to see if it happens with O'Halley's last update too.