Are you sure you used plain VFAT16 to format them?
In my experience (SAM440EP Flex with OS4.1u2) almost all of the USB-thumbdrives I tried worked flawlessly. Two however refused to show up on Workbench. I have noticed that you can corrupt the filesystem, if you remove the stick too early when writing data.
The progress bar on Workbench is apparently no good indication. I have grown into the habit of waiting an additional minute before removing the thumbdrive and had no data loss since.
