mixed rates

Does anyone else have issues with clients being offered mixed rates with mixed cancellation policies?

 Often clients are offered first night at standard rate ( one night deposit required) , then following nights at lower non refundable rate ( all to be paid at time of booking) .

 Then the prepayment details request first night deposit only, balace 4 days before arrival.

 Why am I offering 10% discount for full payment up front then not being able to charge this to client until 14 days before check in????

 I ask so many times for this to be sorted out, and the reply is 'that's what the algoriths do'! 

Does any one else have this problem, or can advise how to resolve it?