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Zoom in on your timeline (using the + key) at the spot where your clips meet.
You likely have a couple of stray frames of video hiding in there.
Steve has probably nailed this problem, but there is another consideration, when applying Transitions. For nearly all Transitions, one will need Handles on the end(s) of the Clips, where it is to be applied. These are extra Frames, before, or beyond the set In & Out Points in the Clips. This will explain Handles a bit more:
If one does not have adequate Handles, two things can happen: Frames from what the user thinks are from the next scene can appear, or PrE will warn you and duplicate the last Frame of the Clip to provide Handles. This can cause the scene to "judder," in an unintended manner.
Handles were easier to grasp, as a concept, when one could only do A-B Roll editing, where they could see the Clips overlapping to allow for Transitions, as the Clips were always on separate Video Tracks. With NLE's like PrE, editing is most often done on a single Video Track, and one does not see the Handles. This will give you an idea of what things look like in A-B Roll editing:
Hope that this helps, and saves the problem, when confronting Clips without adequate Handles.
Hunt, when the in-point on my clip is the very beginning of the clip, sometimes I have handles and sometimes I do not... why?
Usually, when the handles are present, and I bring in a transition between two clips, the transition lays right on top of the end of the first clip and the beginning of the second, which is exactly what I want.
In this case I have a slide show that I've exported from the Organizer as the first clip and a short Quicktime video as the second. When I bring in the transition between the two it will overlap the slideshow but not the QT clip. Must I shorten the QT clip to make handles appear and have the transition overlap? (can't try it myself just yet)
Must I shorten the QT clip to make handles appear and have the transition overlap?
That is basically the answer to both questions. Now, some Transitions, like Dip-to-Black can work with shorter Handles. You might want to explore this particular Transition, as it just might get you something usable, if Trimming the Clip is not something that you can live with.
With Clips that have the In, or Out-Points at the first, or last Frame, Trimming the Clip(s), will get you the necessary Handles.
It is advised that one start the camera slightly before any required action, and then keep it on for a few seconds, after the intended scene has ended. I like to leave about 3 sec. of Handles on each end of every scene.