Just a small observation, don't know if it is relevant at all in this context: My new Transcend 32GB USB3 sticks come with no less than four partitions, if I am to believe fdisk -l output (which I tend to do).

Code:
   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1   ?   778135908  1919645538   570754815+  72  Unknown
/dev/sdb2   ?   168689522  2104717761   968014120   65  Novell Netware 386
/dev/sdb3   ?  1869881465  3805909656   968014096   79  Unknown
/dev/sdb4   ?  2885681152  2885736650       27749+   d  Unknown
So, I start with wiping them all and creating one 32GB FAT3 partition, using plain old fdisk.
Have had no problem booting any computer with plain Knoppix-to-flash installation on the repartitioned sticks so far. (Such USB3 sticks also work much faster on USB2).