Same here. 
I have a 1 TB external HDD from WD. I wanted to use one of the two partitions 
to make a Karmic live USB. The program listed three entries - the smaller, 50 
GB partition "sdb1" (which I selected, as it was empty), the 950 GB partition 
"sdb2" (which I used for storage purposes) and the whole physical device "sdb". 
I clicked "Format", and an error came up. Sadly, I didn't write it down. I do 
remember it was fairly technical. Convinced that something went wrong and 
nothing happened, I tried to mount the drive (just in case, heh), only to find 
a single, non-accessible (because it was in use) 1000 GB volume in the "Places" 
menu. I checked Task Manager and found mkfs.vfat and dosfsck working happily in 
the background. 

before: 1 TB external HDD - 2 NTFS partitions; one 50 GB, empty; the
other 950, filled with 500 GB worth of backups of varying importance.

after: 1 TB external HDD - 1 FAT32 partition; empty, just shy of
terabyte.

Interestingly enough, the disk appears to be empty and thoroughly
unusable even for the program's intended purpose of making a bootable
live USB. But that's the least of my worries right now.

-- 
Should warn that formatting will erase the entire contents of the device (all 
partitions).
https://bugs.launchpad.net/bugs/446891
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