Aha I found the problem... when Mamiya0taru changed the way cargo was classified he forgot to update the definitions of contraband.
I stopped factions from scanning if they had 0 applicable contraband items...
therefore-- no factions ended up scanning...
You can probably guess the location of the currently fixed units.csv though it's pretty well tested and the problem has been eliminated.
To add insult to injury, I decided to eliminate scans during battle with a common enemy. (i.e. confed won't scan you if he's fighting with someone other than you)
And lastly I found the problem with your enemies "talkin friendly".... apparently if you were TOO hostile to them, the hostility "wrapped around" and became friendliness...the reason I hadn't seen this is that in the starting game people were really friendly.
But now that I was testing with your game I rapidly saw some friendly comms from kilrathis... aha! problem solved... but only in an executable that I haven't compiled yet... guess that's saved for tomorrow