Welcome to Nikonians! I can't think of a reason that the revised firmware could disable the connection with the battery grip.
Have you tried cleaning the electrical connections on the grip and in the camera? You could also try disconnecting the third party battery grip, installing the battery in the camera and use it for a bit, then reinstalling the grip and see if it works. Good Luck and Enjoy your Nikons!
I recently purchased a cheap grip, and it is on the way here. I expect it in the next couple of days. I'll post the result of if it works or not. I have already updated my firmware (right after I ordered it).
I received the Mieke/Neewer grip, and it works fine with the new firmware. I have real Nikon batteries in each side right now, but have some cheap replacements on the way. I will be testing to see if it will work with just the cheap ones in it, or if ti gives an error. I'll post again once I see what battery configurations work and don't work.
For now, what is known is that the cheap grip works with real Nikon batteries with the new firmware on the D5100.
I received my batteries and charged them up. I inserted both and got the "Incorrect Battery" message. I then inserted the original Nikon battery in the left side, and then the cheap one in the right. I saw the green LED light up and go out, then took the original battery out, and inserted the other cheap battery. The camera worked fine on two cheap batteries then.
For me, when I use it with the grip, I'll probably use the cheap batteries, and when I go without a grip, I'll use the original Nikon batteries, so that I can get the maximum amount of shooting time.
Just thought i'd mention i had the same issue. Purchased an after market handgrip, and 2 'gray market' batteries for the D5100. Worked great until the firmware update. I tried the last posts suggestion in inserting the original battery by itself in the grip, turning it on then off, then inserting other battery. Took a little more fiddling with mine in moving the battery into the different slots, but now its working again.