hmm, you know when you intially have to find the stuff that uses your mac adress, and gives you stuff like Vcount and all that crud? Well, I know for most people it will say your "actual" time offset was 1 second, which is why you start a second earlier. So its possible if you were like me, your actual time offset was 2 seconds, and you have to start 2 seconds before your time.(I'm assuming you are taking into account any button presses you may have to input when they game starts, if not..well, there's your problem)
Personally, once I redid my actual time offset and got it down to one second, I usually find I hit my seed better if I press A towards the later part of the "extra second". But really, you just have to find what works best for your ds/cartridge combo.
Since I had that problem as well, just make sure hatching that egg goes as quickly as possible to minimize how much time you're wasting on frames you didn't hit. So, I'm assuming you do, but having something with "flame body" speeds things up infinitely.
Also, for when you do hit the frame, many people including myself have found that using chatter once when finding your starting frame is more accurate then not. Not sure why, but it does seem to help.
Lastly, make sure you have everything inputed correctly. That includes the minimum and maximum IV frame at 8, the method set to b/w breeding, the parent's IVs(make sure you didn't forget if they have EVs).
Like I said, be patient, I've found 90% of the time its just a stupid error on my part. Good luck.