Had a very similar thing happen with my sky box when i got a new LG tv at xmas.
1) Skybox > Onkyo Amp > TV = Delay
2) Skybox > TV > Amp = No Delay
Switched over to using the 2nd setup and it has worked great since, the amp just gets the audio over ARC and it's happy.
I'd tried all different things even using an optical cable for the audio direct into the amp and it was still lagging behind or in front and every channel was different.
1) Skybox > Onkyo Amp > TV = Delay
2) Skybox > TV > Amp = No Delay
Switched over to using the 2nd setup and it has worked great since, the amp just gets the audio over ARC and it's happy.
I'd tried all different things even using an optical cable for the audio direct into the amp and it was still lagging behind or in front and every channel was different.