I had the exact same error, I tried all the different methods to clone my existing esxi 5.1 on a usb key (winimage, usbit, and loads of others I found) and none worked for me, I just kept receiving the same error:
Bank5: invalid configuration
Bank6: not a VMware Boot Bank
No hypervisor found.
However this free software below *does* work, perfect copy and boots straight into esxi 5.1
http://www.easeus.com/disk-copy/home-edition/
When you click on download it takes you to cnet, click the 'Direct Download Link' text (NOT the Download Now button as it appears to be a different installer & my av software flags it)
I then ran the disk-copy software and it creates a bootable usb key (think you can create a bootable cd not sure)
Then boot into the newly created usb key or cd (ensure both your current usb key and your new usb key are inserted aswell)
Then select disk copy (not partition copy)
Select the source esxi 5.1 usb key
Then select your new new usb key as the destination
follow the prompts to copy
and wait..
Job done, no more head aches