I had the same problem and found a solution.
Flexslider duplicates the first and the last slide when these settings are used animationLoop: true, direction: slide.
These slides got added in the wrong place, outside the <ul class="slides"> instead of inside the ul.
This is how i fixed the problem:
1. Open "captain-slider.php" inside the "wp-content/plugins/captain-slider/" folder.
2. On line 115 you will see "smoothHeight: true,"
3. Add selector: "ul.slides > li" on the line below
This should fix the problem.
If you want you can change useCSS to useCSS: true. This will make the slider more mobile friendly. And if you don't like the slider "animating" its height when the slider loads you can set smoothHeight to false, smoothHeight: false. But don't change this setting if your using images with different heights inside the slider.
Hope this helps!