Effects and transitions in FilmCutter's editor share a selection list but they are two distinctly different things.  Effects operate on frames within a given cip or scene and transitions operate on end frames from a proceeding clip/scene and the beginning frames of the following scene or clip.

T Click the ' T ' button to open or close the transition and effects selection window.

Transitions reside between scenes and therefore a transition cannot be the first or last scene element but are a scene element in themselves, whereas an effect such a FadeIn is applied to a scene and is part of that scene element.  Transitions draw two scenes together and need to be surrounded by usable frames.  If scene one is 30 frames, scene two is 30 frames and the dissolve in between has a duration of 60 frames "?8/(!@)" (error, error, error).  Trust me.

Open the drop down list and click an item to select. Remember fades are part of a scene and transitions like dissolve and wipes are added alone between scenes.  This maybe a little confusing but if you error FilmCutter will help you though it (or try).  The default value for an effect or transition duration (how many frames are involved in the fade or wipe) is 60 frames.  A fade out of 60 frames duration would fade to black beginning at the last 60 frames of the scene.  Dissolves and wipes overlap the scene before and after the number of frames specified as duration. I hope to simplify this soon, or at least make it more obvious. If you select add wipes another window will open allowing you to preview wipe transitions before selecting them.