This is due to the incorrect selection in the field on the Allowance / Deduction known as Tax Certificate Code.

Go to Setups | Payroll | Allowances(Deductions) | Maintain and adjust the Tax Certificate Code to fit the situation.

Do not show on Certificate – This does not show at all, usually used for reimbursement of expenses and normal personal deductions like HBF.
Include in Tax Certificate Totals – This is included in the gross figure. Items like Leave Loading fit this category.
Itemise on Tax Certificate – This prints item by item. Items like union fees and other items that can be claimed and therefore separate figures are required fit this category.