I didn't mean for my post to come across as accusationary, it was just throwing out some possible ideas, that's all.
An explanation of how I know we have nothing which can cause bad eggs:
Bad Eggs in ROM Hacks are almost always caused by usage of Variables and Flags which conflict with the box storage RAM. In Beta 3.1, there was plentiful usage of such vars and flags.
The reason Beta 3.2 demands a restart from an older beta, is due to the fact that we actually repointed these variables and flags into a brand new, clean memory location. I personally rewrote the routines so that only the known safe vars/flags would be accepted, or our new safe vars/flags. None of these share memory locations with the box or Pokémon data, which is the traditional cause of bad eggs, as with every setting/clearing of a flag or setting of a variable, it was possible to accidentally overwrite Pokémon data, which, in turn, meant that the checksum would no longer be correct, and as such, the Pokémon would become a bad egg.
If you follow that explanation (hopefully you do), you will see that only memory modification, through cheating or direct modification using VBA's memory viewer, is the only remaining possible influence.
Again, I'm not accusing you of cheating, but there's nothing in the coding of the game which would allow this to happen, so it makes no sense to us that you're reporting bad eggs, especially when no-one else appears to be.