Two comment boxes required on cart page but only one shows on order confirmation?

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Ive recently developed a store for a client ( and the client wanted TWO comment boxes on the cart page. One box for a gift card message and the other box for order comments. The client also asked for a check box for the customer to tick if they want gift wrapping. The client has just informed me that when a customer checks out she is not being notified or shown when the customer ticks the gift wrapping box or writes in the card message box! She said she is only being shown the comments that are typed in the "other comments" box. Can anyone please help me on why this might be happening and what i can do to fix it?