I'm having a bit of a problem here, too, namely with the Freelancer IFF.
I have a mining-type ship, with mining-type turrets, and a mining-type ID. I go to the Barrier Gate station, do a double bribe, get Freelancers full green. I undock, and my Freelancer rep is right back down to absolute-neutral. Is the Miner ID repninja'd? Or did that crazy lady on the Barrier Gate station just rip me off?
As it is, I'm IFF-less. So I'm getting no bonuses.
EDIT: Oh yeah, there's a Mining Mod Feedback thread for this kind of stuff isn't there? I guess I should have posted this there. Well, too late!