One cause of this is the Visible Transmittance (VT) of the windows in the building, which affects the amount of daylighting provided and this affects how effective the daylighting controls will be in their ability to reduce the electric lighting usage. The CEC CBECC engine accounts for this by modifying the energy usage of the Standard building in response to the VT of your window selections. Please review the Prescriptive Envelope criteria for window VT to see what the budget building is using as the reference VT.
A second cause is you have large spaces subject to daylighting provided via skylights and windows as outlined in Section 140.3 of the code. This section calls for daylighting openings to be provided in a space and your lack of those daylighting openings results in more electric lighting usage than the Standard building.
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