The Employee Commissions report includes only the revenue from items that are eligible for commissions. Whereas, the Therapist Earnings report (Organization Revenue report) includes revenue generated irrespective of your Commission-related settings. This is the reason why the figures on these two reports may not match.
 
If you want to award item level (Services, Products, Memberships, Packages, Gift Cards) commissions, you must first select the checkbox "Allow commission on this service" (Item). For example, to award commissions on a particular service, go to Admin > Resources > Service > (Select a Service) > Select the checkbox Allow commission on this service > Configure other commission-related settings as required > Save.

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