I work on 747-400's and I can tell you that the noise you heard is very normal! Sometimes its more noticable then others, dont know why! Maybe if they are using the center fuel tank it absorbes some of the noise or something! LOL!
As for the Avod, you say its only a little thing....I can assure you it is anything but! The cost of replacing an IFE system with AVOD, even if it is only a hardware upgrade is significant and it also requires the aircraft to be grounded for a time while the work takes place. That is why so few airlines actually refit old aircraft with AVOD, most aircraft with AVOD nowadays you will find were delivered with it already installed. AVOD is still a relatively new thing in the grand scheme of things.
You must also remember that the 747-400 is an old aircraft. It is based on an aircraft designed in the 60's, the first 400 rolled out in the 80's and although Virgin has some of the newer airframes, some only rolling out in recent years, they also have some oldies!