For Blu-ray, I'd make sure you've disabled the Panasonic's bass management. The Model 990 can take care of that for you, but if the Panasonic is trying you may be getting some undesirable double bass management.

For FIOS, have you verified that the box is set to output Dolby 5.1? I've had cable boxes that sometimes downmixed to PCM stereo, which might mess with the low frequency output.