Are you using Sage 50 2015 or newer? See KB 10611:

Note: A new feature was added in Sage 50 2015 that allows the calculation of tax to be turned on/off per employee.

To enable tax for one employee:

1. Open the employee record.
2. Select the Taxes tab
3. Make sure Calculate Tax has a checkmark.
4. Select the Personal tab
5. Verify the Birth Date

Creating the Paycheque:

1. Open the Paycheques journal.
2. Create a paycheque as you normally do.
   

3.  After earning amounts are entered, click on the Taxes tab.

4. Verify whether the EI and CPP tax boxes are white or grey.
   1. If they are grey then automatic calculations are on.
   2. If they are white (i.e. editable), then Sage 50 is set to calculate manually.
5. Select the Calculate taxes automatically icon on the toolbar if not greyed out.
   

Handy Tips:

• If the Calculate taxes automatically button is greyed out, you may not have access to this feature because of your service plan status. Contact sales at 1-888-261-9610 to purchase a payroll plan.
• If you increase the income, check the taxes. Anytime you modify an already posted cheque, you must also click the icon to recalculate taxes.
  

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