Well, I have no way to explain that clear actually.
It's just that, sometimes you land on a split or alternate spread instead of the desired non-split.
Snorlax for example, is always non-split at my game, but on my girlfriends game, she sometimes hits alternate spreads when breeding a Snorlax.
Also, when one of the two parents is RNG bred on a alternate frame, the baby has to be bred on an alternate frame as well, 9/10 times.
I suggest you to experiment with a physical Pokémon. use Frame 15117 (31/B/A/21/31/A, non-split, 4.11.95) and look for an alternate frame that is close to that in time (so 4 minutes plus or less). RNG two parents that would give 31/31/31/x/31/31 on the non-split and alternate frame.