hello there
i got the same issue, i guess it's a bug;
the way i found is a little bit tricky but at least can be used until a stable release ;
apparently the uuid of the clone is not changed automaticly by the mod. and it should ; ) you have to help him a little bit
depending where you save your clone (server or client), manage to edit the file (any text editor) in the custompcs/clones folder (you will see inside the tabulation folders and then your clone file)
ie in case of server : .minecraft/world/customnpcs/1/squeezie
1) then find the line with something called "UUIDLeast":
that should look like : "UUIDLeast": -4697947154252137166L,
2)change the number : ie
"UUIDLeast": -4697947154252137167L
3) save the file (and do not quit the text editor)
4) clone your npc ingame (once)
5) go back to step 2) or quit..
a little bit tricky but better than nothing.
i don't have noticed second effect with this method. but of course is not doable with spawner.
have a nice day