A few questions:

What input do you use with the BDP-51? Is it using the analog 7.1 Direct input? If so, you can't change audio modes because you are bypassing the DSP.

Did shutting everything off and turning it back on help? If the Harmony got confused but has worked in the past, this should help resolve matters.

Does the 990 trigger the 7125? If so, could you have switched to an input that has the 12V trigger disabled for some reason? That would shut the amp off.