I have a Sony STRDA5400ES, with a Tivo Premier getting tv off air, and a Directv HD, both connected by HDMI. On some tv channels, I get no center channel, and the sound has that "out of phase" quality. I live where I can get 3 markets clearly, and on each of the 3 stations with missing center channel, I can tune to the same network program from another city and the sound is correctly placed, indicating that the receiver is working properly at least for those stations. When I plug in earphones, the receiver switches to headphone mode, and the sound is centered and in phase.
I wrote to one of the stations, but got no reply.
Before the Sony, I had a Pioneer Elite digital surround for several years, connected by toslink, and never noticed lack of center or any out of phase feeling.