Multiple Pokemon in Box -> Bad egg

[Dystou]

I have created 30 Pokemon for Box 1 in Pokemon Black with PokeGen. For the whole Box 1 I have generated AR codes and exported all of those codes into an XML File, activation is L + R.

Using the AR Code Manager software I have inserted these codes into my Action Replay DS. When I pressed L + R Box 1 was filled with 16 Pokemon (I can only activate 16 codes at once), although the first one ended up as a bad egg. When I used the other 14 codes, the first Pokemon of those 14 was a bad egg again. I have tried this multiple times with different Pokemon and it has always been the first Pokemon that ended up as a bad egg in the Box.

On a side note: On my Pokemon Black version I can NOT open the Pokedex, the option is not available even after getting the National Pokedex.