I don't see what the problem could be. You could try to bring up the menu the first time (so the frame advancement before you talk to the daycare man and before you do the chatter advances is the same), but I don't see how that would change things. Hacked Pokemon may make a difference, but I'm really not sure. I would try getting a legit Japanese Ditto and see if it changes things.
Other than that, the only other thing to my knowledge (which isn't very large when it comes to RNG) that could be wrong is bad luck with the Timer0.
And thank you!