One you can try is HxD.
Under the Extras menu, you'll see an Open Drive choice. It will pull up a list of logical and physical drives. I'd use the physical and make sure you're selecting the correct drive (it will show up as a removable drive).
It's a bit tricky to use. But, it's got the ability to select blocks on the drive itself, and use some features under it's Edit menu to fill the space with 00 (fill selection).
It's a bit tough to use for this purpose (it took me a few tries to figure it out when testing with a CF Card, since I was getting mismatches between the selected bytes and how many I wanted to fill with 00's),
I don't know if that would do any good or not (trying to fill the first part of the drive with zeros and repartitioning using Windows Disk Manager tools and letting Windws recreate the MBR).
That's a trick I've seen others mention for drives that didn't work. But, it seems to me that using another tool to overwrite the MBR like Ranish would accomplish the same thing (and using Ranish to create a new MBR works fine with CF cards in my camera).