If the item discount percentage applied to mrp instead of list price, then check the discount structure configure in BUSY by folllow these steps:
Step 1: Go to administration section then click on configuration option.
Step 2: Choose voucher series configuration then select the required voucher type like sales, purchase etc.
Step 3: Select the series of voucher then click on voucher configuration tab which appear in right side for screen.
Step 4: Now, check the configured discount structure and select discount structure for percentage to list price and save the configuration.