I had the same problem. I gave up after a few days of trying every imaginable fix I could think of, and even called presonus tech support, who said I probably had a defective unit, so I kept the good one and took the other back. I probably should have just exchanged it for another one, but I had a bit of jingle in my pocket and was gassing for a new guitar, so I used the store credit and some money and walked out with a sweet Gibson SG, heh.
My old StAudio soundcard works with the firepod, but it just doesnt sync up right. I can use them both together if the instruments are totally unrelated, like say drums all on the firepod and some scratch guitars on the stAudio, but damn it would be nice to have 16 inputs for drums.
But yea, just make sure everything is updated, and you follow the most recent installation instructions you can find (I think theres a different method for the newer firmware) and if that doesn't work, call presonus, and they should be able to help you out better. From what I've read, though, syncing up two firepods is supposed to be easy as pie, so maybe you got a lemon like I did.