It sounds to me like you're using a different feature - Fusion has the built-in feature that it will stop doing something if there was no trigger, or in some cases "only one event" will not run again until there is a trigger. (It's why I avoid using that command.) It sounds like you're getting that scenario - where you're using "only one event" to make something not happen until that trigger. But the pause - activate / deactivate is interfering with that.
If you're not using the built-in pause then as you say, you'd have to set flags or values to control it yourself - unless you have a moving object or action that you can control or test against rather than flags i.e. if the object hasn't moved.