Originally Posted by Completely Clueless
Then I loaded the Clonezilla Live files onto this boot partition.
What do you mean you loaded the files? To create a bootable device you need to change the boot partition of the device. This cannot be done with a simple copy command.
From what I understand your thumb drive still has the PM bootsector loaded. (Installed by PM to create and change partitions on reboot)
There are various ways to fix this. I think the quickest would be to use UNetBootin to extract your iso onto the thumb drive and will also correct the bootsetor. http://unetbootin.sourceforge.net/