I think that Jam does pretty well against Baiken in AC. I play that matchup against Hellmonkey's Baiken every now and then, and it seems like Jam has quite a few advantages.
Baiken is usually on the other side of the screen, airdashing back with j.S or tatamis. Typically, all Jam has to do is get above Baiken's max height in the air by superjumping and doing 236P at the apex of your jump, then airdashing toward Baiken and coming down with j.H. But, if you have 25%, all you have to do when you see Baiken jump backwards is FB Puffball. It'll go under her jump and hit her before a tatami comes out as long as you did it fast enough. As long as you were in front of Baiken when she began her IAD backwards, the tatami should fall right in front of Jam. As soon as you see Baiken leave the ground, it's OK to use a FB. Also, I don't think it's a good idea to use FB Puffballs unless Baiken is in the air. She gets a free combo if she blocks it and counters.
On the ground, if you ever manage to get close by scoring a knockdown, Jam is almost always able to block counters by ending a short gatling in 2P. Like, 5K-2P, 6K-2P, or 6P-2P. I've even blocked Baku before, and that shit is mad quick. You can punish Baiken's 412S and 412P counters if you block them with a 2D into 236S-K, then charged 236K or whatever. A 2D should also hit the 412K counter where she goes behind you. If she does the 412H crossup counter, I'm not totally sure but jumping back with j.S might hit her out of it.
After a while, the Baiken player should stop countering your short gatlings, and you can start using tick throws after a blocked 2P. If you're in the corner, and you want to FRC your throw into Jam's 6H-H loop, start with 2H-6H after the FRC. Baiken flies up really high if you use 5S-2H-6H for some reason.