My time differential is +1. So, I have to hit things at :25 to get a :26 seed, etc.
What I mean exactly is that, when I'm hitting something at :25, I need to hit it so that the DS menu fades away exactly as the "click" for :26 happens in order to get my timer0 consistently.
It takes some practice and experimentation. It also may vary for your DS.
It also could be my imagination. ^___^