are you sure that the files you repacked were the japanese ones ? you could use toxpack to extract the new files (header+ w/e the other is) then compare them to the extracted euro, there should be some size differences.
if you are 100% sure the new files got in the new pack and u are sure that the japanese files were correctly renamed before getting packed, then have you cleared game data from the ps3 so it reinstalls the game once you launch it ? unless that is done it wont take the new files in. and also i hope you remembered to rename the new files as they get made with an extra "_repacked" in their name which needs to be deleted