I had something like this yesterday.
Are you using the usb as the clonezilla boot device. In which case as I am sure you know you change the bios to boot the usb hdd device (F12 boot menu).
Yesterday I booted my minipc with clonezilla (as above). When it gets to the bit asking where you are going to store images and to store stuff and you select "local devices", and it prompts you to insert your storage usb and press enter, well I put my usb storage device in, it recognised it, I pressed enter, and it did not see the usb storage device when asked. So I cancelled the process and tried again, then it saw PINKY (for that is the name of my usb storage device, not to be confused with RED, by clonezilla usb boot device). No idea why, just so.
Perhaps run some tests on the problem usb to see if it is picked up. If pclos can see and mount each usb device then they should be good for clonezilla.
Plan B - format it to ext4 rather than FAT
Plan C - how about saving the image via ssh to another box (test you can ssh as root before clonezillaring)