I also had the problem of crackling and distortion, which would only happen occasionally, but I was able to resolve it with help from Outlaw Customer Support.
It turns out that the DSP chip in the 990 is very sensitive to heat buildup. I had the 990 right on the top of a 12 channel amplifier, which would almost start glowing red after being on inside an MDF enclosed rack all day. Suffice to say, I believe that the sensitive chip cannot handle any heat above what the 990 itself produces.
I'm not so sure that this is a serious defect in design as it is just the nature of high-end electronics. This doesn't mean I think there should be a fan in the 990 either, after all... AV equipment should be properly ventilated anyway.
I would love to hear if other people have found evidence to suggest that this is in fact a fix. All I know is that when the 990 temp. is normal, the distortion is gone!
I hate to say it, but I don't think that it has anything to do with inputs or settings. It didn't matter if I unplugged it, reset it, or left it on! The only variable which is absent when it works is warmth! It is purely an environmental factor.
Weird, I know, but easily solved with some well placed 12v computer fans, wired up with a 3.5 mini plug and plugged into the 990's 12v switched output. (Don't forget to enable the switched output in the OSD!)