The phantom game bug is when you can't write a new game to NOR on the 3in1, and when you try to delete the game from NOR AKAIO says there is nothing there. The fix for it is to use another flashcart to write a game to the 3in1+ or use something like the NDS backup tool 3in1 to backup a small game to the 3in1+, thus erasing anything in NOR and SRAM automatically.
You can use the SRAM test to reset the contents of the SRAM, it should be preformed on a flashcart that doesn't have problems with homebrew.
If you don't have a second flashcart, it would be wise to get one for fixing purposes if nothing else.
If the AK2/i is your only flashcart, use the official firmware to run any fixes. If you don't want to use the official firmware, you will need to use the ak2_sd.dldi from the official firmware file and replace the one in the AKAIO folder, otherwise you will ALWAYS have issues running some homebrew including gba exploader.