If the issue happens before X is even loaded, then that means it's not an X bug.
It sounds like plymouth (or perhaps grub or something else in the plumbing layer) put the GPU into a bad state, and so when eventually X came up, it couldn't fire up 3D on it, thus no effects.
You might try booting earlier alphas of natty to see if you can bracket when it started.
If the issue happens before X is even loaded, then that means it's not an X bug.
It sounds like plymouth (or perhaps grub or something else in the plumbing layer) put the GPU into a bad state, and so when eventually X came up, it couldn't fire up 3D on it, thus no effects.
You might try booting earlier alphas of natty to see if you can bracket when it started.