NOW: I will "clone" the whole USB stick again, I think I did not copy the MBR (?), Just the PBR from the stick.
You cannot copy the MBR too (or you will effectively re-partition the target).
You need to copy (not "clone", "deploy" - provided that the tool you are using allows that) the volume, then adapt the data in the MBR, PBR to the new location on target and finally rebuild the ldlinux.sys.
Folow me for a moment.
Imagine that the USB stick is only 1,000,000 sectors in size.
When you use YUMI on it, it will make a MBR with a partition entry for a FAT32 filesystem starting on sector LBA 63 and size 995967 sectors (or whatever below 1,000,000 that respects CHS boundaries).
The PBR of the filesystem will have as data 63 sectors before and 995967 sectors in size.
The ldlinux.sys will contain similar data.
Now if you "clone" the "whole stick", it will overwrite everything (up to 1,000,000 sectors) on the target.
The "target" will likely work but will have only one partition (and any partition that was there before will be lost).
If you instead "clone" the "volume" only, the area on target might be EITHER:
1) exactly the same addresses (which implies that among the other partitions you already created one starting on LBA 63 and 995967 sectors in size)
2) different addresses, let's say starting at LBA 2,134,598 (and possibly enlarging it to 3,148,875 sectors)
If #1 everything should be OK, BUT the Disk Signature will be different (cannot say if this is relevant to the booting), possibly you will need to recreate/refresh the ldlinux.sys anyway
If #2 you need to:
a. have the different target addresses as a valid partition entry in the MBR
b. correct the start address (and the size if you changed it during the "clone"/"deploy") in the PBR to reflect the new, different address to which you wrote the "volume" or "superfloppy"
c. recreate/refresh the ldlinux.sys
It is entirely possible that the software that you are using is capable of doing a. and b. above automagically, but surely it won't do c. that has anyway to be done manually.
In the worst case you will need to do all the steps a., b. and c. manually.
I hope I made the matter a little bit clearer.