I am having the same problem! I properly charged the deposit to the liability account.  That makes perfect sense.  Now I have created the invoice and I entered the amount of the deposit in the deposit box right below the invoice total, so the invoice balance reflects that deposit.  But when I save the invoice, I get that message that says I have to specify an account to credit the deposit to, but it does not tell me how to do it.  It's driving me crazy!