We have thousands of customers so having a system in place to show instant payments especially for direct debits will take some time to show on our system as cleared.

That is by design @Lee_EONNext and nothing to do with the amount of customers. Someone somewhere has taken a deliberate decision to have a system that delays the DD amount being shown as credited to the customers account by several days.

I know of two major companies that do the opposite, they show the DD amount as being credited at least 24 hours before the DD is actually taken. So it's clearly nothing to do with the number of customers.