If the problem is as wolverine just stated, my suggestion is not the best solution. But if the problem is really a balance of levels, has anyone tried this?

If the up-sample vs. bypass subwoofer level is too high in favor of bypass and you relied on the 990’s automatic calibration, turn the gain down slightly on the subwoofer and recalibrate. The 990 should respond by increasing the output to the sub for digital modes to restore the sub’s acoustic output to its former level. Meanwhile, when no digital management is occurring in bypass mode, the sub’s level will be less. Compare up-sample to bypass again. If the sub’s level is still too high in bypass, repeat the above procedure. If the sub’s level is now too low in bypass, increase the gain on the sub, but not as high as it was originally and, again, recalibrate. Repeat the appropriate portion of the procedure until you have a balance.

If the up-sample vs. bypass subwoofer level is too high in favor of bypass and you use a meter or RTA for setup, measure and find the difference in the sub’s level between up-sample and bypass. If the result is 4dB, then lower the sub’s gain by 2dB and increase the 990’s subwoofer digital level by 2dB, then test again.

Eventually you should find a point at which the level with the digital features engaged balances almost perfectly with the throughput in bypass mode.