Best bet here is to factory reset the device. Take out the SD card while this happens.
Reformat the SD card's partitions on a PC while the phone resets. For myself, I used GParted in Debian Linux to create the partitions and to format the SD card.
Once the reset's done, turn off the phone, put the card back in, turn on. You'll need to log on to Google, and if necessary, reactivate the phone. When the launcher is fully up, reinstall your programs. I'm assuming you don't have a backup, so you'll have to go to Google Play Store, and put them all back one by one. (If you can, restore wifi before downloading from the Store so you don't have to use 3G.) If you have a backup, install the backup app, and then reinstall.
Nannycrick, partitioning the SD card is normal practice for Android users who use custom ROMS, or just root phones to take advantage of extra functions not available in unrooted form. The second partition is meant to store programs that would normally reside in the phone's internal storage. Then a program like Link2Sd is used to create symbolic links in internal memory. This method has been in use for years among various UNIX based OS's.