I have to admit, I don't know if this is a new "feature" or not - I just installed the newest FanFixes patch tonight, and tonight's when I noticed the problem. But it could certainly be coincidence.
My fighter has been missing critters left and right all night long, and it was making me angry. So, I decided to take a closer look at his stats screen. He's level 6, and here's what I see:
If he's barehanded, his AB is +6
If he's got a nonmagical weapon, his AB is +10; apparently strength doesn't get added in until you're armed?
But, using his +2 spiked chain, his AB is +9. Furthermore, when I unequipped the chain in order to investigate, sure enough, the red box shows up and he's not proficient.
Thing is, that's the first feat he took as a human level 1 fighter, and it still shows up on his feat listing. Nonetheless, he can't use the damn thing anymore.
Now, I have to say, I've been pretty unimpressed with the whole Tripping ability, so if necessary, I'll use the Python command to hack the crap out of him and give him a +2 lonspear or something instead. But I thought I'd ask if anyone else had seen this, and what could be done about it if they had.