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.
I have to go so I can't help you alot more today, but this is what you have to do
Select a target frame and make sure the parents have the right A and B IV's, then save in front of the daycare man. Now you have to softreset and let emloop run at the same time. now talk to the daycare man until the sentence take good care of it'when Emloop almost reaches 00.00.00 you make a save state (Read: ALMOST, you have to land before your target frame, but as less as possible). now pause your game load the save state you made and press Ctrl + Z + P at the same time (This let's you unpause your game while finishing the take good care of it sentence at the same time). Now check the IV's of your egg and put them in RNG reporter. If everything is done correctly, you are very close to your target frame. If you landed 160 frames before your target frame for example, pause your game again, load the save state and press ctrl + n 160 times. Press ctrl + z + p and find yourself having a flawless pogeymon.
Your frame is determined once you finish the daycare man's sentence: Take good care of it. Then put the egg in slot 2, determine it's IV's using RSEdecoder and put those IV's into RNG Reporter (Use Emerald, no split) or by using Wichu's PokéRNG (The old version).