I think I have found the answer but I am yet to test this to confirm. The trophy folders for the game's I have trouble with seem to be missing a directory.
The correct folder format should be: PS3_GAME/TROPDIR/NPWR00429_00/TROPHY.TRP (This is Colin Mcrae Dirt for example. KOF XII and the other games I have the same problem dont have the NPWR00429_00 file folder or whatever folder name the game will have e.g PS3_GAME/TROPDIR/TROPHY.TRP.
If anyone having this problem can test this and let me know would be much appreciated The only problem I have is finding out the folder names for each games as my Blu Ray drive has packed in