Your sub clipping may be due to a known issue with the 990's subwoofer test tone - the tone is full-range. The recommended workaround for powered subs is to turn on your subwoofer's internal crossover and set it somewhere near the upper limit (150Hz or 200Hz) before running the test tone, then go back to bypassing the internal crossover afterward (since the 990's bass management takes care of it for everything except the sub test tone). Another option in your case is to manually set the sub using a test tone from a DVD like Video Essentials or AVIA.