You still probably making the same mistakes as before, your just patching everything that isn't SRAM, 0.58b can already handle most games that support flash 512 (It can run the pokemon games that use flash 512 without issue, it just can't do anything about the RTC).
You need to delete those saves on the microSD and erase the copy of the game you got on the 3in1 and erase the save on there by writing a game that works. Use and run a clean rom, don't even bother to patch it, ExpLoader should automatically patch it for you.
The other possibility is that your using a hacked rom of the game that has the same CRC info or hash check. In this case you will have to dump your own copy of the game for this.