There are some well buried HDMI settings you might check in the PS3 under sections where you might not expect them.

Are you using the same cable when swapping back and forth? How about a HDMI switch in there. I had a similar issue with a cheap HDMI cable when I introduced a switch box. Straight through it was fine but I lost audio if the switchbox was in the mix and other cables worked well with the switcher. Seems that some HDMI cables just have electrical limitations and once you add in a weak element, they fail.

With great power comes Awesome irresponsibility.