Suggested fix (unconfirmed): Enter a new room with Lovelace in your party to force the gallery to register her final level. Do not discard the upgraded girl until you have entered this new room.
Suggested fix (unconfirmed): Queue another damage converter after Akiko to change her poison damage into another damage type with its own multiplier. Alternatively, pair poison damage with smoke and use laser, gauss, or jet modifications to manage range and projectiles.