Not sure how to re-encode a video that was created in Vyond (if that matters?).
There is a click box on the slide that runs the rest of the slide. I was trained to include one on each slide of a CPT project. It's minimized and sits in the upper left corner. Could that be interfering?
Oh no.... too many incompetent trainers. Click box is almost gone, since it is not supported by Fluid Boxes. Moreover, it is meant to pause the slide. Its pausing point is at the end of its timeline. You do have a pausing point, although you told not.
Please take out all those click boxes, Captivate is not a PPT, a presentation tool where each slide has to be paused at the end (and there are lot better ways if you really insist on that). Sorry for my answer full of frustrations but I hate it when I hear ' I was trained to....' and then a stupid workflow.
It is that click box which is causing the pause at the end. Delete it and if I could, would dim the Click box totally 
As for re-encoding: you have to open the Adobe Media Encoder, drag the video file to the window top right. Normally the output codec will be indicated automatically (H264) and you just have to click to get the encoding started. But you'll not need it here, delete that click box.
When you have time, you could read this post:
Pausing Captivate's Timeline - Captivate blog
Have much more articles about timeline, but this is the most important.