I have a similar problem, as I wrote an OS to a flash drive hoping to use it as a boot disk, and now can't format it back to 2 gigs. There's a 1 gig partition on it that Linux doesn't seem to touch.

It became a headache after I found out my computer wouldn't boot with it, and I couldn't format it to get the space back.

It'll take me some time to recall what OS it was, as I've tried out about a dozen different flavors over the past week.

It may have been a Live version of GParted or possibly Haiku.

Anyway, fdisk -l lists it as /dev/sde
so I did dd if=/dev/zero of=/dev/sde

and I just got back 1 gig, not 2.

I've tried the latest GParted with no success, either.

If I had to guess, it was probably Haiku, as I think I followed these instructions to make it-
http://www.haiku-os.org/guides/making_haiku_usb_stick

this is what worked for me. i inserted the flashdrive on the USB port then got a OS cd inserted on the cd drive and restarted my pc as if i am wazs going to install teh OS then when it showed me the disks and partitions i selected my flash drive there were two partions i deleted both and then there was only one unallocated space partion. then i cancelled the installation,that gave me back my 8 gigs. but make sure you select your flash drive and not you c drive because then you will really have to reinstall the OS.