I like the (my) idea that Lavos waits as long as possible before he decides he must ravage the population in order to carry out the next step before he can be stopped. So, when he deems humans almost technologically advanced enough to stop him, he calls it good, destroys the planet, and then moves on to creating and sending out Lavos Spawn.
Or maybe he waits until he's discovered, and that's when he calls it. Maybe some research scientists found him and he said okay, time to call it... boom, Day of Lavos. He did something similar to Zeal (kingdom) when he noticed they were messing with him. Lavos wasn't having any of that, so he destroyed the place. Only in 1999, they're living in domes, all across the planet, probably have the internet... so Lavos decides it's time.
Because remember: billions of years of work would be lost if he doesn't successfully send his spawn out. It's pretty safe to assume that he wouldn't risk failure.
Alternate theory for fun: maybe he waited for the top species (humans) to stop evolving. He wanted every last bit of natural selection... and when they became so technologically advanced, survival of the fittest truly didn't apply anymore. With humanity no longer evolving, no need to keep collecting that DNA... boom, Day of Lavos.