Depositing Pokemon through the "Deposit" function in the PC as opposed to the "Move" function will not heal the Pokemon

Throwing everything into the PC and withdrawing them for the battle Vs. East in the Jade Tower. No Nurse Joy there so I put one Pokemon through the Move function in the PC and it healed. Tried the rest through the Deposit function and it didn't heal. Withdraw function isn't the problem since I used it both times.