An at beginning of scene action should trigger all actions inside of it that are not wrapped inside of an if query. If there are any actions inside of an if query then those actions will only be triggered if the query condition is met.
What exactly are you trying to do? & are you willing to post some screenshots of the at begin of scene action?
Just to clarify: animations that are on infinite loop should unload at the end of the scene. Jump to x action part loops on the other hand will not unload at the end of a scene, which is why it's a good idea to wrap them in an if query.
if condition 'some_condition' is true
add some actions here
jump to action part #1
Something like that & then when you want it to stop looping you just change the condition value, or you could use the quit action action part if the loop was started inside of a called by other action.