It looks like the actual video file that Kap saves has slightly smaller dimensions from the settings.
For example, I set mine to 1280x720, and here's the Get Info panel for that file.

The dimensions are _1276x716_ (4px smaller in each direction).
Thanks fo the report, @stursby! I had that I mind but completely forgot about it. We'll make sure to include a fix for it in the next patch! 馃槃
@stursby On a side note, could I ask how the size of the window got that small? If it's a bug, I need to fix it.
@CodeTheory which "window" are you referring to?
@stursby The Kap window in your screenshot looks off.
Here's yours:

Versus mine:

Your window is somehow thinner than it should be.
It looks like the window is changing widths after toggling the Controls panel. You'll notice the scrollbar show up, then quickly disappear. Here's three states:

Hope this helps!
Whoa @stursby, that's really strange. Could you open an issue for it so we can discuss? 馃槃