In transactions which involves huge quantities (monetary as well as physical instruments), the basic systems and control should be in place. Solution which I would recomend is:
A) System and control: - along with the cheque details, there should be a column in the software to update the bank's deposit slip number. As the bank's deposit slip number is an internal but serialised document, the same cannot be tampered with. - In the evening all the cheques along with the summary which is updated in the bank's deposit slip should be handed over to the bank's colletion agent. - The bank's collection agent should match the entries in the deposit slip number with the physical instruments handed to him and give an acknowledgement. - The acknowlegement should be faxed to RMS the same evening. - This procedure kills the chance of making entries in the system without the physical instrument in hand - This process also gives a check on the materialiazation of cheques. As the bank gives credit deposit slip number wise. The internal audit can immediately pin point the transaction showing variance between the banks credit vs the credit shown in RMS
I think this process not only provides a day-to-day control but also saves time to track variances on occurence.