OK, I thought it was easy to repro ... it seems to be related to adding and then deleting entries.
Try this
1) Format USB
2) Copy two iso files
3) Launch EasyBCD and load BCD onto USB
4) Create an entry for each iso
5) Confirm entries
6) Delete both entries (this is what causes the problems)
7) Add entries for both iso again
8) check entries (I see THREE entries)
I know its not quite the same as the original problem but it's related I think because of step 6