Are all the HDMI inputs on a TV the same? On my Panny 37PX80 I seem to get a slightly better image quality if I connect my Sky HD box to HDMI 1 than if I connect it to HDMI3
Well, there is a Sony receiver with one HDMI marked for Blu-ray Disc input, as the designers say this has the shortest signal path and thus gives the best quality, so I guess the same could be happening on your TV.
Please note I am offering an observation, not an opinion, before all the 'digits is digits' jockeys jump on me...
Are you using the same the picture settings for both inputs? I don't know if it's typical (I always assumed it was) but my TV has separate memories for each input. If the settings are the same then I'd tend to agree with Andrew.