My personal experience with 990's auto setup was less than stellar. It was, most probably, confused by room reflections, which are very bad in my case, and the distance 990 came up with(for the channel closest to the wall) was rather the one to the wall than to the speaker.

I'd recomment that you set the crossover back to 100 Hz for your surrounds and perform the auto setup again. If the distance to your sub is messed up, input the real one.

Auto setup is, in my view, only a convenience. Nothing beats a tape measure when adjusting the speaker delay.