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That's pretty mysterious. The file opened fine in Windows/whatever?
I can't think of anything else except to reformat the thumb drive using FAT32 and trying again. The only other possibility (I can't remember the kernel version used by the PE) is to make sure the drive isn't formatted in 64kb allocation blocks. (There were some older Linux kernels that puked on a 64kb block.)
What's the brand/size of the thumb drive? Does it have something goofy like U3 on it (a useless security partition)? Is the PE plugged in when it updates? Some people have recommended that, although I admit I updated unplugged right after I charged my PE out of the box.
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