Sometimes when I use a Flourish charge the enemy only takes damage from the last swipe.

I have tried this with AT on and off. I have noted that if an enemy is directly in front of the player then the charge will push the monster along with the player but they will not take damages from the stabs just from the last swipe.

The only way for a Flourish charge to be fully successful is to let the charge go at a distance, as such the flourish charge is not as reliable as any other sword charge in the game.