Crap, that must be due to the newly-added IFF mod. Can you mantis everything?
There are lot of Problems regarding Default IFF, I have some missions where Aspect Seeking Missiles can lock to Friendly targets, another problem is that I get a "Team: " or unfilled data Team in Missions that Team are set right, you just get into a text editing and you can see its okay.
In FRED2 Debug Build it reports there is no Default IFF for any Species, it doesn't matter if it is specified in the Species_def.tbl or the -sdf.tbm, it just ignores it, and keep reporting it (the same for Colour and AWACS Multiplier)
Also sometimes it messes team, like you set it to "Friendly", but it appears in "Red" colour, maybe it's only messing colours......
I am using Inferno........but the CVS Build is the Standard (non-INF)