We need a bit more information.
Was the narration part of the captured video?
Was the narration on a separate audio timeline?
If the narration is on a separate timeline, when you place a transition on the video timeline, it has to overlap the two video segments in order to do the transition. This of course will shorten the total length of the video. An equal amount is removed from the end of the audio timeline so that it's total length is equal to the video. The audio track will no longer be synchronous with the video, after the transition.
The proper way, is to make all of your video edits, including transitions, and then lay down your narration.
If this is the case, and it is all complete, you will either have to re-do the narration, or it might be possible to cut out segments of the audio and slide the remaining audio timeline to synchronize it with the video. If, when you are doing video editing, you lock the audio track, nothing will be removed while editing.
If I have misunderstood the problem, give us more information.
Don