I have exactly the same issue. The partition is still there, but for some reason ML is unable to select if for boot.
Here is how to solve it:
Check that the paretition is still there. It should show up on your desktop, otherwise check with disk utility.
If it is then:
0) If there is any essential data on it, copy the data to another drive, just in case the below doesn't work. Also make a backup of your OSX partition and data to be on the safe side. All should go smoothly, but we're talking computers, so pelase make sure you backup everything before.
1) Get Winclone from TwoCanoes (it's a great utility which will help you if you want to upgrade your HDD without having to reinstall Win)
2) Use Winclone (make sure it's the latest version, compatible with Mountain Lion, not one of the old free ones) to backup your Windows partition. You can back it up on your OS X partition, it's just one file. Ideally do it on an external HDD, it will be faster.
3) Use Bootcamp assistant to go back to one partition. Your Windows partition will be deleted, and you'll be back to have only one OSX partition taking the whole HDD
4) Restart
5) Use Bootcamp assistant to create a new Bootcamp partition. You can use the opportunity to change the size of the Windows partition to make it smaller or larger than it used to be. Winclone doesn't care about the size when it restores, so it doesn't have to match. Don't redownload the tools, and don't install Windows, it's not necessary. When Bootcamp assistant has created the BC partition, stop it before it installs windows and reboot.
6) Use Winclone to restore your bootcamp partition.
7) Restart, and hope for the best...
Let us know if that worked for you as it did for me.