My setup: I have two HDMI cables going into HDMI 1 and HDMI 2 on the Samsung TV. I have two video sources (a Moxi DVR and a FIOS STB) connected to 2 different inputs on the Sony. When it does not work, I cannot get either HDMI 1 (when connected to HDMI out on the Sony) nor HDMI 2 (when I swap cables) to deliver a picture. However, each HDMI cable is fine and delivers a picture when connected directly to the video source.
I have to believe that either (a) the Samsung and Sony are not compatible (seems unlikely) or (b) something is wrong with the HDMI connection to the Sony from either the input source (not likely, especially as I get sound) or the HDMI out. I have tried an alternate cable and it had the same problem. Also, when I move the SONY to a different TV, it works fine.