I have just finished playing Uncharted Drakes Fortune. (I know, I'm a bit behind) Anyway, I noticed that although I did receive the medals in the game I did not receive any trophies for the game. The trophy menu does show up but it says I have 0/48 when I clearly should have earned at least a few. I am connected to the internet and as far as I know the game is as up to date as possible and I have never been asked to patch it. I bought it in December and just started playing so I assume the patch just downloaded into the game when I was installing it. I've scoured the internet looking for answers so maybe you can help me.
Are you using the original version or the greatest hits version of the game?
Also, check your game data utility folder on the PS3's main menu. You should see a file in there for the Uncharted patch. If it's not there (or, even if it is), I recommend deleting all data relating to Uncharted (both game save files and game data files) and trying again, making sure the update is in place.