You hold them down from the moment you start the game until after the logo. If that's not the problem, check your adjacent seeds, make sure you aren't hitting the wrong Timer0 or something.
I am sure its not my Timer0 because I have been using the same timer0 and have successfully RNGed all 3 of the musketeer trio, Zoroark, Zorua, Victini, and Volcarona using seeds from the same timer0 value. I think its probably the button thing that is messing me up. I got one on Frame 1 where I only have to hold Left so I will hold left on the dpad right after I start the game until the years for the game show up.