Go into the issue report about Final Fantasy Crystal Chronicles and grab the SaveState for the VBA-M. If you use that, it'll work like a charm. There are other issues, but it will at least be playable. Basically, after you load the GBA bios in your steps, just load the savestate next, then start a new game.
Edit: Decided to not be lazy and get the link: https://dolphin-emu.googlecode.com/issues/attachment?aid=31770045001&name=bios_state1.sgm&token=k-svbCtmHp7s5sjKTqR1FZfp7xs%3A1385955022129
Edit: Decided to not be lazy and get the link: https://dolphin-emu.googlecode.com/issues/attachment?aid=31770045001&name=bios_state1.sgm&token=k-svbCtmHp7s5sjKTqR1FZfp7xs%3A1385955022129
