Well, nobody can verify this issue with vicfg-cfgbackup.pl?

I cannot get it to work, but I have figured out how to make a backup of the USB Flash Drive, here are the steps;

(The issue/problem was that the partition table was in GPT format, not the normal/older MBR)

I use Clonezilla in vmware player, and connect the USB Flash Drive to the PC before starting Clonezilla;

Backup ESXi USB drive
=====================

Save GPT Data to disk:
------------------------
$ sudo gdisk /dev/sdb
Hit p (Check that you are on the right disk)
Hit b (back up GPT data to a file)
Enter backup filename to save: /home/partimag/ESXi2_Build_914609_130130_GPT.bin
Hit q ( .. yes, to quit)

Save data from the USB drive
-----------------------------
sudo dd if=/dev/sdb1 bs=512 of=/home/partimag/ESXi2_Build_914609_130130_sdb1.dd
sudo dd if=/dev/sdb5 bs=512 of=/home/partimag/ESXi2_Build_914609_130130_sdb5.dd
sudo dd if=/dev/sdb6 bs=512 of=/home/partimag/ESXi2_Build_914609_130130_sdb6.dd
sudo dd if=/dev/sdb7 bs=512 of=/home/partimag/ESXi2_Build_914609_130130_sdb7.dd
sudo dd if=/dev/sdb8 bs=512 of=/home/partimag/ESXi2_Build_914609_130130_sdb8.dd

Restore ESXi USB drive
======================

Restore GTP Data to new USB drive
--------------------------------
$ sudo gdisk /dev/sdb
Hit p (Check that you are on the right disk)
Hit r (Recovery)
Hit l (load partition data from a backup file) (Might get a message complaining about drive size, ignore)
Hit w (write table to disk and exit)
Hit y (to confirm)

Restore data to USB drive
-------------------------
sudo dd if=/home/partimag/ESXi2_Build_914609_130130_sdb1.dd bs=512 of=/dev/sdb1
sudo dd if=/home/partimag/ESXi2_Build_914609_130130_sdb5.dd bs=512 of=/dev/sdb5
sudo dd if=/home/partimag/ESXi2_Build_914609_130130_sdb6.dd bs=512 of=/dev/sdb6
sudo dd if=/home/partimag/ESXi2_Build_914609_130130_sdb7.dd bs=512 of=/dev/sdb7
sudo dd if=/home/partimag/ESXi2_Build_914609_130130_sdb8.dd bs=512 of=/dev/sdb8

... but I really like to get vicfg-cfgbackup.pl or something similar (remote or local on the esxi host???) to work, as its done online, with the above procedure, the vm's and the host has to be offline ...