Russ,
I'm not sure of what incompatibilities exist, or why one port works and another one wouldn't. There is an extra process for the dual input that, for a reason I can't explain, works in this particular application.
It is possible that you may get better results by changing the output resolution in one of the other connections.
--HDTech
I bought a Samsung LE40A556P TV from the Dixons website just before Christmas. I also purchased a Philips DVP3980 upscaling DVD player and a HDMI lead from Sainsbary's. I connected the Philips to the TV using HDMI 1 and I had the following problems. The picture was noisey, It had white lines going up the picture and the sound was rapidly coming and going, as if someone was turning it on and of very fast with a switch. I tried HDMI 2 and the picture was perfect but the sound problem was still there. I finally tried HDMI 3 (which Samsung say to use when using a DVI - HDMI lead, which I am not) and both sound and picture are perfect. Has anyone got any ideas as to what the problem is here? I have not been able to try another HDMI lead as I have not got one. I was not sure if it was a compatibility issue between the Philips and the Samsung. It says in the Philips manual that the HDMI out is HDMI CEC complient.
Any help with this would be appreciated.
Russ.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic