Anyone use Digital Juice ETKII?

Hard to picture exactly what you're saying, but I'm imagining the clip they gave you has a black background. If so, simply drop your chroma key FX into the clip/transition, then select black as the color for it to key out (use the eye dropper & drag a section of the black background of the clip to match it more accurately. It should get rid of the black you're mentioning, and allow your track underneath the transition clip to show through at the right times. Hopefully that helps.
 
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