Look, the MBR contains both boot code and the partition table, you asked about cloning the partition table, then you stated that you cloned the boot code, and then you are talking of a full clone, and later of the partition boot code.
You might want to try to explain better the issue at hand and what you actually tried exactly, making sure you use the proper terms or better explain in your words the situation.
A clone is an EXACT, integral, copy of course if even a singe byte is different between source and target it is not a clone anymore.
Without knowing what OS is that, how it boots, which particular hardware is involved, what is the final goal, what exactly happens etc., etc. we will just make wild guesses at it.
As a side note (not necessarily your case) some (badly coded BIOSes) will only accept up to a given size of USB stick.
For all we know the *whatever* you are running may make (say) a checksum of the *whatever* it writes to the USB stick and this will make any modification to it detected and discarded.