Your pump output program is missing the Set ON command. Don't confuse Fallback ON with Set ON. Fallback only applies if the module loses communications with the Apex, such as when the AquaBus cable is disconnected, while the Apex is rebooting, or if the Apex locks up for some reason. The Set ON command is needed to tell the pump what to do if the If Maintenence line is false.
Change your code to this:
Fallback ON
Set ON
If Output Maintenance = ON Then OFF
See my Apex Tutorial series for more tips:
https://www.reef2reef.com/ams/authors/suncrestreef.93940/