What operating system are you using?
The schedule at is a basic schedule that runs directly within FlashFXP where-as the Tools > Schedule is more advanced using the windows task scheduler to start FlashFXP perform the task and then close.
The only thing I can think of off hand is perhaps FlashFXP failed to start via the task scheduler, you can review the task scheduler log via the windows Task Scheduler this can be launched via the windows Run prompt (Windows key + R) type schedule and then look for the FlashFXP scheduled tasks.
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