Maybe this is more of a general PS3 question but never the less. So i downloaded the new update for the game and started playing. I got a confirmation saying i unlocked a few Trophies but when i go and look at them in the XMB it still sits 0% and says i have unlocked nothing! so, um what gives? Also do Trophies unlock  retroactively?

You should start a fresh game after the download. If the trophies are unlocking and they aren't appearing in the XMB, you should probably quit the game and let the information synchronize.

Go to your trophy collection and re-sync.

I have synced the game twice. No go. I guess if i really want them i need to start with a fresh save. man i really don't want to play the game on Hard again! Ahhhh. Now with that said do you think i should just delete all my uncharted system data so i can really get a fresh start? or is just starting the game over again be good enough?

starting a new save should be enough.

Ok i will give it another go later! Thanks every one.

Dude, Hard isn't that bad.  I ran through the 2nd time in 4 1/2 hours.  Now I'm 33% though on Crushing in 45 minutes (skipped movies).