The ground loop is probably associated with the cable from the dish to the box. With cable TV service, the solution is a ground loop isolator (the best typically being the Jensen), and I think a similar approach can be used with satellite. Other satellite users around here may have specific isolators that they've used.

Modern surround receivers and processors simply don't have an equalizer loop like older stereo gear used to. The only real option is to go in between the 990's pre-amp output and the amp's input.

The component inputs will only be visible on the component output - the inputs are not converted down to composite and s-video - so you'll need to be viewing the 990's component monitor output to see the component inputs. If you do that, do you still not see the component inputs?

Good tip on the 7" LCD monitor...