The Parallax Background feature doesn't work with video. It can only be applied to single images and InDesign elements.
However, there is a workaround that you can use to simulate a parallax effect with video.
You can leave a page blank in your scrolling document where you want the video to appear. When you export it (in5 > Export HTML5 with in5...), go to the Backgrounds section and set both Background Color and Page Color to None.
Then in separate document, place the video. You might set it to Auto Play, Mute (mute is the workaround for some browsers that restrict auto-playing video without user interaction), and Loop in the in5 Video interactive widget (in5 > Interactive Widgets > Video).
Make a rectangle with no stroke and no fill on the same page above the video. With that rectangle selected, embed the other scrolling document using the in5 Web Content interactive widget (in5 > Interactive Widgets > Web Content). In the Web Content dialog, click the button with the 3 dots to navigate to the index.html file of the other document.
The video will auto-play behind the other scrolling content. Because there's no background or page color in the scrolling document, the video will show through when the user gets to the blank page.
I show a similar setup (it's not exactly the same, but it's a similar approach) in the following video:
