I have my cable box run through the 990 to the HDMI input on my TV. On some channels the sound only comes through the center speaker and on others it comes through the front 3. Why?

The audio format is responsible for that, along with the way that the 990 is decoding it. Some channels that are broadcast in essentially mono, in which case Pro Logic II will tend to collapse the audio to the center channel. You may be able to steer more to the mains if you increase the setting of the Center Width to at least 4 or maybe 5, but even then I'm not sure how effective surround processing will be.

thanks! I am new to this and still somewhat unsure of some of the functions of my 990.