Normally the "effect in" that you set in transition logic should just be a scene director that handles the transition of the scene online (i.e. usually it's quite short). (both the old and new scene will be online during the transition). Longer animations would normally be done on the main scene director. So, the new scene should only be in the transition in for a very short period of time.
In your situation, on the scene with the long transition in, you could Tick the checkbox labelled "Wait for Out Effect". This will make sure the old scene plays offline completely before it starts to transition the new scene online. I think this would solve your problem.
#XPression