You're wrong, I use r4bugfix2 and have deleted all JAP (and the E or U versions that I do not have) games from database using the r4cce08 (cheat code editor). Just read it all again, do everything it says and you will be prevail!
It's also a good idea to always compare the game ID of the rom you are using to the one held in the cheat.dat (you check the ID's using the r4cce08 program). If you are using the same region rom as the cheat, but the game IDs differ, alter the cheat.dat ID using the r4cce08 software and save it.