Clip to clip transitions...

sounds like your using the fade to black or dip to color filter. Check for a flash frame in between the clips. also make sure you have enough room on each side of the clips outside of your in and out points.
 
I would guess its probably a flash frame or not enough handle room on the ends of both the clips. try it on a couple different clips with plenty of room on each end. If that doesn't work maybe trash the pref?
 
What I find strange is, if there's no handles, you can't lay the transition. If the clips are not phycially touching in the Timeline window, you can't lay the transtion "across the clips".

Here's one guess; you have black at the begining and/or end of those clips you're using and need to set in and out points on each before hand.

OR you mean the first clip fades to black and the second clip just pops in? Folks, we need y'all to be specific on these forums, provide details! If this is the case, then they are not touching, as the Capt says, and you're only applying the transition to one clip, not both. Zoom in on the Timeline closer (Cntl with the plus key) until you can see the detail of the two clips coming together.
 
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