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tl;dr -- You should replace "Window1_KXS1_act" with "Window1_S1_act".

I think the issue is that you have a mismatch of EMS:Actuator names. Here is what I have gathered from your EMS code:

• The schedule that you are trying to change is named BLDG_KXS1_WINDOW1_Jones_2017_SCH
• The EMS:Actuator object changing that schedule is named Window1_S1_act
• Window1_S1_act only appears in Line 1 of the EMS:Program object named Window_Jones_2017 (set Wind_Cur_State=Window1_S1_act, !- Program Line 1).
• Later lines in the same EMS:Program object are using if/else logic to set 0 or 1 to Window1_KXS1_act -- a slightly different name that has an extra "KX" compared to the original EMS:Actuator created.

In short, you are never actually overriding the schedule value because the EMS:Actuator name isn't entered correctly in EMS:Program lines. You should replace "Window1_KXS1_act" with "Window1_S1_act", and that should fix it.