That's weird, that never happened to me... I guess I'm lucky.
I know some ways of solving that problem, but some of them could be a pain.
1*If you have another PS3, create a new user, link that user to your PSN account (choose "I already have an account" or something like that when you register on PSN and enter your PSN address and password). After that, don't sync your trophies. Start playing the game and get the combo trophy and the story related ones, synch your trophies to PSN. Go to the PS3 you actually use, synch your trophies there and you should get the trophies you couldn't get before.
2*If you have an external HDD but don't have another PS3, back-up your data with the PS3's backup utility. Then format your HDD, create a new user, create a PSN account by selecting the "I already have an account" option. Start the game from the beginning, get all the trophies, synch your trophies after that. Then format your HDD, restore your old data with the external HDD and the backup utility and synch your trophies again to get all the trophies you synched before.
3*I don't know if you can create another user in the same PS3 that uses the same PSN account you're already using, if you can do that, you won't need to back up/format/restore.
4*Maybe it could work if you just delete the save data and the game data if you installed it an start the game all over again from the beginning... but I don't know if that'll work.
I'd try with number 4 first... if that doesn't work (try getting the 100 combo trophy to see if it does, you can get it in the beginning specially if you play on hard, it's the fastest way to check if it actually works) then try number 3... if you can't create another user with the same account info as the user already created, then you'll have to either go for number 1 or 2 depending on wether you have another PS3 or an external Hard Drive to back-up all your data... or if you have both, then choose whatever you think is more convenient for you.
I really don't know what else you could do. I'm sorry if I couldn't help. Maybe someone else can give you a better option.
You could try getting online if you want, but I doubt that's the reason the trophies didn't unlock... you're supposed to earn them even if you don't get online.